The worst one I've been caught by was with git submodules. I had a submodule for a project on github. The project was unmaintained, and I wanted to submit patches, but couldn't, so I forked. Now the submodule was pointing at the original library, and I needed it to point at the fork instead. So I deleted the old submodule and replaced it with a submodule for the new project in the same commit. Turns out that this broke everyone else's repositories. I'm still not sure what the correct way of handling this situation is, but I ended up deleting the submodule, having everyone pull and update, and then I created the new submodule, and had everyone pull and update again. It took the better portion of a day to figure that out.
What have other people done to accidentally screw up git repositories in non-obvious ways, and how did you resolve it?
