It was so endemic in Chicago that it was standard practice to withhold last month’s rent and send the landlord a letter saying to take the security deposit and send you a bill for any repairs.
This is both against the lease and financially equivalent to what an honest landlord would do, except the burden to get paid is now on the landlord.
If they have kept your security deposit in a separate, interest bearing account as the law requires[0] there should be no problem in the transaction.
0. Hahahahaha there was exactly one landlord I had who actually did this (not in Chicago) and returned my full security deposit with interest.