Usually one of two things, mostly the latter: I forget to exclude all the .git/ directory from the sync, or I have in-progress and nowhere near ready for commit changes on both hosts, and I forget and sync before I check. These are all PEBKAC problems and/or workflow problems, but on a typical day I'll be working in or around a half-dozen repos and it's too easy to forget. The normal git workflow protects from that because uncommitted changes in one can just be rebased easily the next time I'm working in that on any given computer. I've been doing it like this for nearly 20 years and it's never been an issue because remotes were always quite stable/reliable. I really just need to change my worfklow for the new reality, but old habits die hard.