Unfortunately, yes, there are a few places were files can grow unbounded. We're working on tying up those loose ends:
1) Database logs under the logs directory
2) DBxxxx folders under the default arcgisportal directory that get created during failover or import site
3) walarchive logs in the backup directory that can grow unbounded once you run the DR tool. They are cleared out when you create a full backup
4) Service logs, (the Windows service logs), but this is fixed as of 10.6