This has been mentioned before but that’s no problem Monzo are working on a solution -
AFAIK, the only workaround to deal with this now, is the increase the Category’s Target by the amount that was repaid, to cancel out the debit. You don’t need to increase your Total Monthly Target, as the repayment is picked up by that. Obviously updating the category’s Target is a pain, especially if you need to do that quite often but it would enable your Target’s alerts & performance against target tracking to work as expected.