Hi bksansoo,
Thank you for the kind follow up and additional information.
Is this occurring to all of your mailboxes which you have rules for, or does it just seem to be a certain mailbox?
Just to isolate the issue a bit further, could you try creating a new mailbox and applying a new rule to see if emails can be moved to this new mailbox? If this works, but some of your other mailboxes do not, it could mean there is some sort of damage to the path. If this is the case, it may be best to create a new Mailbox and move your existing messages to it.
Do you use any other email accounts on your Mac? You can also test the behavior with other email providers to isolate the issue further.
If this doesn't help, or if the issue seems to apply to all of your mailboxes, this may be best handled in a direct support case with Apple Support. You can review support options at the link below.
Get Support - Apple
Thanks for using Apple Support Communities! Feel free to reply to let us know the result of the above steps. Take care for now.