You probably didn’t notice in my last post, but “log file” was a link. 
Here it is again: Where is the log file located?
Hm, that would be really weird if it’s the exact same issue because the GitHub issue I’ve linked was specific to folders. As @overheadhunter has mentioned there, the problem is that Cryptomator fails because the folder it tries to delete is not empty.
If you can find any errors inside the log file, please let us know.