Use git check-ignore command to debug your gitignore file (exclude files).
In example:
$ git check-ignore -v config.php
.gitignore:2:src config.php
The above output details about the matching pattern (if any) for each given pathname (including line).
So maybe your file extension is not ignored, but the whole directory.
The returned format is:
<source> <COLON> <linenum> <COLON> <pattern> <HT> <pathname>
Or use the following command to print your .gitignore in user and repo folder:
cat ~/.gitignore $(git rev-parse --show-toplevel)/.gitignore $(git rev-parse --show-toplevel)/.git/info/exclude
Alternatively use git add -f <path/file> which allows adding otherwise ignored files.
See: man gitignore, man git-check-ignore for more details.