Enemies scale with days passed? Really? Tell me does the game inform you of that at any point?
Oh, that one is actually pretty clever:
There are two main kinds of scaling in the game: Edicts and Wanted enemies. There might be some general scaling (
EDIT: there is, confirmed by people checking the code.
The minimum-level also raises per-floor), but if there is it's pretty slight.
Wanted Enemies will start spawning once you reach a certain point in the game. Their main gimmick is that each time you meet and defeat them, they will gain a level and get stronger. They give an order-bonus for subjugating them, but there is no way to get rid of them permanently, meaning you have to keep proggressing through the game to keep up with them. Their max level is 50, and the game tells you about wanted enemies and their number once you have built "the office" (not recommended early in the game)
The second way is just through the various edicts that affect enemies. The gimmick here is that each time you clear a floor, the "problem"-edicts for that floor's enemies will be automatically enabled, which you have probably noticed makes them a bigger pain. The problem-edicts are the main reason battles become hard, especially trying to deal with stuff like Thugs, Rogues and buffed-up Lizardmen. Picking Solutions is usually among my priorities while playing, especially when I'm not playing a build that can handle those kinds of threats. But you'll also probably notice that there are always downsides to every solution...
Beyond ones for individual enemies, you can also pick Edicts that just generally give "inmate stats+", and edicts that give "Rare enemy+", making spawns of "special" enemies, for the most part higher statted ones, more common. Almost all of these are tied to giving you more income, making it a pretty straightforward risk/reward with the caveat that you can't go back on anything but the first-floor "admittance-policy". One of the early "hidden" ones is actually building a mess-hall, since that stops weak "starving" prisoners from spawning, but the rest are all labeled, to my knowledge.
The last thing that influences difficulty beyond that is the ammount of enemies, which the guards clearly tell you is based on the level of order in the prison. Less order means more prisoners.