git
looks at the content of a file.
Modification dates are a trigger to indicate that the index should be recomputed, but if a file has the exact same content at the same place, it will not appear as "modiified".
In order to confirm that the files have different content, you can look at the hash that git computes :
# get the hash for the file in the current commit :
git ls-tree HEAD path/to/file
# compute the hash for the file on disk :
git hash-object path/to/file
If the hashes are equal, you may have hit an issue where the index wasn't properly refreshed, try running :
git update-index --refresh
to have git re-check all files (note : if files still appear as modified after that, please add a comment or update your question, there would indeed be something weird going on)
If the hashes are different, the contents are definitely different. You will have to look closer at what changed between the two versions of that file, for example by comparing the hex dump of each version.