1. It kills machines on startup. My machine had the CPU and HDD maxxed out for 30 minutes every time I started it, rendering it unusable
2. You can only sync a single folder, which is really limiting
3. The syncing algorithm is crap (well, it was for me anyway) - I was constantly resolving conflicts incorrectly
4. Probably a continuation from point 2 - it actually deleted files it shouldn't have
I'm mostly happy with Seafile. I've had a few issues from time to time with the Windows client, but overall a much better experience than with Dropbox.