After All For One pretty much blew up an entire district in his battle against All Might, one may question the police's ability to imprison him (he is alive and in some sort of iron maiden). On that note, there are probably other notoriously powerful villains with quirks that would make it easy for them to escape from prison.
What measures do the police take to control villains with all sorts of quirks? Perhaps the iron maidens are capable of disabling them?
Another example is when they find Nomu. They just put some handcuffs on him. Hell, the only reason Nomu didn't escape is because it was in a docile state.