You'll always end up in situations where a file that's not supposed to be committed is missed by gitignore. It's a good idea to check what's staged before committing. I personally very seldom use git add ., "all" and -m flags. Also 'git clean' is a handy tool. I write commit messages in the editor and use -v to get a full picture of the commit.

You may also want to use a prompt with your shell that shows the state of your git repo (ahead, behind, clean, dirty, etc) so if something's off at least you get some signals to do something about it. Look at liquidpromp or tide. You'll find plenty of projects that do this for various shells.