Despite not having a spam filter active (at least, not one I have been able to find settings for), I am finding spam e-mails from one of my IMAP accounts deposited in the trash of my POP3 e-mail. Since my IMAP accounts all have trash folders (and junk folders, but that's beside the point), I think it would be more appropriate to have them deposited in the trash folder of the account to which the e-mail was addressed. Also, if there's some default spam filter, there ought to be settings for it somewhere to define this sort of behaviour. If this is a general Claws-Mail bug (I used the SpamAssassin plugin when I was using Ubuntu), I will repost there if necessary.
I just noticed that the spam functionality I was noticing was from a filter using the mark_as_spam action. It did not, however, include any move action so my point there remains the same. It should also be noted that I do not have a spam plugin and cannot use the mark as spam/ham buttons or menu entries, yet can utilize their related actions via filters.
This has been fixed in 3.12.0 by changing the "mark_as_spam" action to only mark the message and not move it. You can move such marked messages wherever you want using additional filtering rules.