These files should not cause any issues, but this has been reported so that they do get removed. What options do you have selected on the agent to see the "~"? Are you using AV?
Thanks for reporting this issue. In the meantime, we will probably script the removal of these files as part of our agent deployment. As far as options selected on the agent, we are pretty vanilla; not much customization. We plan on evaluating Kaspersky AV, so that is enabled. Again, the "~" directory does not appear until we initiate a scan from the server side. The folder contains:
/~/Library/Application Support/Kaspersky Lab/KAV
Hopefully this helps.