If you use git, that can definitely help you. The trick is in making small, targeted changes that do one logical 'thing', and then committing that. Don't be afraid to make tiny commits -- often I'll make a series of 1-liners if they aren't strictly related. Commits are very cheap in git, so don't worry about making "too many".
Then when you run into a problem, you can easily use "git bisect" to figure out which commit caused the problem, and if you've kept to small commits, you should hopefully be able to figure out the offending line(s) of code pretty quickly.
But beyond this, I think the early sign is your gut says, "it should be so simple but I can't figure out what's wrong". Listen to your instinct -- it's probably right! Don't spend another 2 hours poking at it. That's a good time to either step away for a bit or ask someone else to look over your shoulder for a bit while you try to explain to them what's going on.
Then when you run into a problem, you can easily use "git bisect" to figure out which commit caused the problem, and if you've kept to small commits, you should hopefully be able to figure out the offending line(s) of code pretty quickly.
But beyond this, I think the early sign is your gut says, "it should be so simple but I can't figure out what's wrong". Listen to your instinct -- it's probably right! Don't spend another 2 hours poking at it. That's a good time to either step away for a bit or ask someone else to look over your shoulder for a bit while you try to explain to them what's going on.