Steps to reproduce the issue

Create a Zip-File witch contain <? and upload it in custom code like descriped in https://docs.joomla.org/How_to_use_the_filesystem_package.

Inside JFile::upload($src, $dest) InputFilter::isSafeFile() is called witch find <? in the zip-file and return false

I created a Zip-File on Macos with two jpg's and the resulting file contains <?
No hack or attack. Just normal use of the Archiver.

Expected result

Move uploaded file from PHP temp folder to filepath stored in $dest.

Actual result

File not moved.

System information (as much as possible)

PHP 7.4 and Joomla! 3.9.23

Additional comments

I fond a way to upload my zip file with following code:

$safeFileOptions['php_ext_content_extensions'] = array('rar', 'tar', 'gz', 'tgz', 'bz2', 'tbz', 'jpa');
JFile::upload($src, $dest, false, false, $safeFileOptions)

Perhaps it is better to search <?php instead of <? beause in PHP-Shorttags are deprecated and not useable by default.