Background

I’m new to git, and I’m testing it as a version control for a website that is not hosted on github. I have made the public_html a git repo and created a bare repo outside the public_html that I push all the commits and tags to. My goal is to be able to tag changes I make to the website and have the option to quickly revert back to previous versions when desired. So far with my testing, I have been able to accomplish this by either using reset or checkout followed by the tag name to go back to previous versions.

The Problem

I encounter problems when I make new version tags that involve removing files from a previous tag. If I try to reset to or checkout the previous tag where the files were once present and functional, visit requests for these pages return "Internal server error". I know the files are there because I see them reappear in the public_html folder (as seen when refreshing cpanel, or filezilla). If I download these files, delete git from my website altogether, and add them back to the public_html folder, they work fine, indicating the files have not been modified or corrupted. Furthermore, when at a tag where the files are indeed removed, I get a "Page not found" result.

Is this a common issue? Any tips, advice, or workarounds would be much appreciated.

Update 1

Based on the kind suggestions of @VonC, I have tried

1. Preventing unwanted EOL changes by setting the core.autocrlf to FALSE.
2. Running git clean.

Unfortunately, these suggestions did not resolve the issue. I have also determined that this issue happens with PHP files but not HTML. I have continued reading up on my own, but I’ve not yet found any reports of a similar issue. I hope to figure this out soon. Currently, I would be unable to revert to a previous version if I ended up removing files and regretting it, which is essentially one of the primary benefits I hope to get from git.

Also, I was curious if git modifies permissions, but I’ve checked, and they’re unchanged.

Update 2

I thought it might be helpful if I specified everything I tried in case someone wants to attempt recreating the problem.

$git init --bare bare_repo.git
$cd public_html
$git init
$git remote add origin ../bare_repo.git
$git add index.html # simple testing only "hello world" 
$git add commit -m "index.html"
$git tag -a v001 -m "v001"
$git push origin master --tags

Now add in a PHP file:

$git add phpinfo.php # again for testing only, includes <?php  phpinfo(); ?>
$git add index.html  #file changed to include link to phpinfo.php
$git commit -m "phpinfo.php"
$git tag -a v002 -m "v002"
$git push origin master --tags

Now, checkout v001:

 $git checkout v001 

The index.html returns back to origin state without link, and phpinfo.php disappears from the public_html folder.

Now, checkout v002:

  $git checkout v002

The index.html regains link, and phpinfo.php re-appears in public_html.

However, when I try to go to phpinfo.php, I get the "Internal server error or misconfiguration" page load.