Steps to reproduce the issue

• Activate SEF in configuration.
• Protostar template.

• Copy files
  /components/com_contact/views/contact/default.php
/components/com_contact/views/contact/default.xml
  to folder
  /templates/protostar/html/com_contact/contact/
  and rename them
  aaa.php
aaa.xml

• Open aaa.xml and change title of LAYOUT tag (line 3)
  <layout title="COM_CONTACT_CONTACT_VIEW_AAA_TITLE"

• Goto backend and create a menu item named aaa of type
  Contacts >> COM_CONTACT_CONTACT_VIEW_AAA_TITLE
  in Menu Item Root of a menu that is displayed on your page.

• Create a second menu item as submenu of aaa.
  

• Create a breadcrumbs module on all pages.

• Check link of menu item aaa in menu: /index.php/aaa
• Open submenu of aaa in frontend.

• Check link of menu item aaa in breadcrumbs module. It contains the layout query part: /index.php/aaa?layout=protostar:aaa

Expected result

Link in breadcrumbs module should remove query string like in menu links.

Same issue with com_tags but not with com_content.