You said in your original post that you are running Fusion 12.2.5 and your About My Mac says you're running Ventura 13.3. If that's the case, you have an unsupported configuration. Fusion 12.2.5 is not supported or tested on Ventura.  Fusion 13 is the first version that contains support for Ventura. That could be part of your problem. Give the Fusion 13 trial version a try and see if you can reproduce the problem. 

>> - but it doesn't delete large files unless you tell it to.

CleanMyMac doesn't have to delete large files to mess things up. Personally I'd stop using CleanMyMac and any other of those so-called "optimization" utilities  They have the potential to really mess something up behind the scenes and you won't know what it is. macOS doesn't need to have itself "cleaned". Use those utilities only as a last resort, IMO.