Detect alignment is uncommon. All spells that have weird mystery-spoiling effects are marked as uncommon. If you let your players pick it and they're using it to solve mysteries they're not supposed to solve you have to either invent contrivances to throw them off ("but you see officer, you the evil you detected wasn't coming from me, it was coming from that cursed vase that I got from Cheliax", "it's not technically illegal to be evil") or you invent consequences for it ("you detect evil on me? okay, I guess I gotta kill you now").