Steps to reproduce the issue

Updated J2.5 website to lastest version of 2.5. Disabled Remember Me plugin. Either updated other extensions to version compatible with 3 or disabled. Upgrade with Components → Joomla Update

Expected result

Successful upgrade

Actual result

Got error:
1062 - An error has occurred.

Duplicate entry '1' for key 'PRIMARY' SQL=INSERT INTO #__content_types (type_id, type_title, type_alias, table, rules, field_mappings,router) VALUES (1, 'Article', 'com_content.article', '{"special":{"dbtable":"#__content","key":"id","type":"Content","prefix":"JTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"title","core_state":"state","core_alias":"alias","core_created_time":"created","core_modified_time":"modified","core_body":"introtext", "core_hits":"hits","core_publish_up":"publish_up","core_publish_down":"publish_down","core_access":"access", "core_params":"attribs", "core_featured":"featured", "core_metadata":"metadata", "core_language":"language", "core_images":"images", "core_urls":"urls", "core_version":"version", "core_ordering":"ordering", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"catid", "core_xreference":"xreference", "asset_id":"asset_id"}], "special": [{"fulltext":"fulltext"}]}','ContentHelperRoute::getArticleRoute'), (2, 'Contact', 'com_contact.contact', '{"special":{"dbtable":"#__contact_details","key":"id","type":"Contact","prefix":"ContactTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"name","core_state":"published","core_alias":"alias","core_created_time":"created","core_modified_time":"modified","core_body":"address", "core_hits":"hits","core_publish_up":"publish_up","core_publish_down":"publish_down","core_access":"access", "core_params":"params", "core_featured":"featured", "core_metadata":"metadata", "core_language":"language", "core_images":"image", "core_urls":"webpage", "core_version":"version", "core_ordering":"ordering", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"catid", "core_xreference":"xreference", "asset_id":"null"}], "special": [{"con_position":"con_position","suburb":"suburb","state":"state","country":"country","postcode":"postcode","telephone":"telephone","fax":"fax","misc":"misc","email_to":"email_to","default_con":"default_con","user_id":"user_id","mobile":"mobile","sortname1":"sortname1","sortname2":"sortname2","sortname3":"sortname3"}]}','ContactHelperRoute::getContactRoute'), (3, 'Newsfeed', 'com_newsfeeds.newsfeed', '{"special":{"dbtable":"#__newsfeeds","key":"id","type":"Newsfeed","prefix":"NewsfeedsTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"name","core_state":"published","core_alias":"alias","core_created_time":"created","core_modified_time":"modified","core_body":"description", "core_hits":"hits","core_publish_up":"publish_up","core_publish_down":"publish_down","core_access":"access", "core_params":"params", "core_featured":"featured", "core_metadata":"metadata", "core_language":"language", "core_images":"images", "core_urls":"link", "core_version":"version", "core_ordering":"ordering", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"catid", "core_xreference":"xreference", "asset_id":"null"}], "special": [{"numarticles":"numarticles","cache_time":"cache_time","rtl":"rtl"}]}','NewsfeedsHelperRoute::getNewsfeedRoute'), (4, 'User', 'com_users.user', '{"special":{"dbtable":"#__users","key":"id","type":"User","prefix":"JTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"name","core_state":"null","core_alias":"username","core_created_time":"registerdate","core_modified_time":"lastvisitDate","core_body":"null", "core_hits":"null","core_publish_up":"null","core_publish_down":"null","access":"null", "core_params":"params", "core_featured":"null", "core_metadata":"null", "core_language":"null", "core_images":"null", "core_urls":"null", "core_version":"null", "core_ordering":"null", "core_metakey":"null", "core_metadesc":"null", "core_catid":"null", "core_xreference":"null", "asset_id":"null"}], "special": [{}]}','UsersHelperRoute::getUserRoute'), (5, 'Article Category', 'com_content.category', '{"special":{"dbtable":"#__categories","key":"id","type":"Category","prefix":"JTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"title","core_state":"published","core_alias":"alias","core_created_time":"created_time","core_modified_time":"modified_time","core_body":"description", "core_hits":"hits","core_publish_up":"null","core_publish_down":"null","core_access":"access", "core_params":"params", "core_featured":"null", "core_metadata":"metadata", "core_language":"language", "core_images":"null", "core_urls":"null", "core_version":"version", "core_ordering":"null", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"parent_id", "core_xreference":"null", "asset_id":"asset_id"}], "special": [{"parent_id":"parent_id","lft":"lft","rgt":"rgt","level":"level","path":"path","extension":"extension","note":"note"}]}','ContentHelperRoute::getCategoryRoute'), (6, 'Contact Category', 'com_contact.category', '{"special":{"dbtable":"#__categories","key":"id","type":"Category","prefix":"JTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"title","core_state":"published","core_alias":"alias","core_created_time":"created_time","core_modified_time":"modified_time","core_body":"description", "core_hits":"hits","core_publish_up":"null","core_publish_down":"null","core_access":"access", "core_params":"params", "core_featured":"null", "core_metadata":"metadata", "core_language":"language", "core_images":"null", "core_urls":"null", "core_version":"version", "core_ordering":"null", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"parent_id", "core_xreference":"null", "asset_id":"asset_id"}], "special": [{"parent_id":"parent_id","lft":"lft","rgt":"rgt","level":"level","path":"path","extension":"extension","note":"note"}]}','ContactHelperRoute::getCategoryRoute'), (7, 'Newsfeeds Category', 'com_newsfeeds.category', '{"special":{"dbtable":"#__categories","key":"id","type":"Category","prefix":"JTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"title","core_state":"published","core_alias":"alias","core_created_time":"created_time","core_modified_time":"modified_time","core_body":"description", "core_hits":"hits","core_publish_up":"null","core_publish_down":"null","core_access":"access", "core_params":"params", "core_featured":"null", "core_metadata":"metadata", "core_language":"language", "core_images":"null", "core_urls":"null", "core_version":"version", "core_ordering":"null", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"parent_id", "core_xreference":"null", "asset_id":"asset_id"}], "special": [{"parent_id":"parent_id","lft":"lft","rgt":"rgt","level":"level","path":"path","extension":"extension","note":"note"}]}','NewsfeedsHelperRoute::getCategoryRoute'), (8, 'Tag', 'com_tags.tag', '{"special":{"dbtable":"#__tags","key":"tag_id","type":"Tag","prefix":"TagsTable","config":"array()"},"common":{"dbtable":"#__core_content","key":"ucm_id","type":"Corecontent","prefix":"JTable","config":"array()"}}', '', '{"common":[{"core_content_item_id":"id","core_title":"title","core_state":"published","core_alias":"alias","core_created_time":"created_time","core_modified_time":"modified_time","core_body":"description", "core_hits":"hits","core_publish_up":"null","core_publish_down":"null","core_access":"access", "core_params":"params", "core_featured":"featured", "core_metadata":"metadata", "core_language":"language", "core_images":"images", "core_urls":"urls", "core_version":"version", "core_ordering":"null", "core_metakey":"metakey", "core_metadesc":"metadesc", "core_catid":"null", "core_xreference":"null", "asset_id":"null"}], "special": [{"parent_id":"parent_id","lft":"lft","rgt":"rgt","level":"level","path":"path"}]}','TagsHelperRoute::getTagRoute');

System information (as much as possible)

CentOS 6
php 5.6.25. Also tested with 5.3
mysql 5.5.52
apache 2.2.15

Additional comments

Last line of update_joomla.php:
2016-09-15T20:40:35+00:00 INFO ::1 update Ran query from file 3.1.0. Query text: CREATE TABLE IF NOT EXISTS #__content_types ( type_id int(10) unsigned NOT.

Followed this for upgrade: https://docs.joomla.org/Joomla_2.5_to_3.x_Step_by_Step_Migration

I've tried removing J1.7 sql updates from update folder but that didn't help.