Comment 3 for bug 1042268

You can change the configuration to ignore them:
http://askubuntu.com/questions/26658/is-it-possible-to-exclude-a-file-or-folder-from-being-synced-while-it-is-in-a-d

I'm not sure if the default should be to ignore them or not. I'll leave this bug open so the people in charge can make a decision.

Thanks for the report.