Support

Hello,

That's the expected behaviour.
Akeeba Backup will automatically exclude folders belonging to Control Version System, such as .git, .svn etc etc.

As previously said, CVS folders are automatically skipped, and for good reasons.
First of all, they will bloat the size of your backup: you're going to include every single change made to every single file, even from years ago.
Then, it's a source massive issues. Let's say you perform new changes to your files, you commit to the repo. Then you restore a previous backup. Now that installation of git has an history that diverges from all other clients, if any complex operation is performed (like rebase or fixing commit conflicts) there's the serious risk to compromise that repository for good.

I strongly suggest you to avoid doing that, however, if you really want, you can add the .git folder as an external folder. Further info here: https://www.akeebabackup.com/documentation/akeeba-backup-documentation/off-site-directories-inclusion.html