Yeah, enemies gradually ramp up in strength if you take too long to kill them (possibly to stop you from endlessly farming free items from reorganizing).
There have been some past issues where people have been essentially softlocked by a certain toad mage in the deep caves who heals all enemies every single turn as well as either shielding themselves or occasionally attacking you. Since healing numbers used to scale over time like with block and damage (IDK whether they changed it or not), players unable to kill the mage before it ramped up would be in a very bad position without some sort of damage scaling. At that point, the only way out is by either dying, throwing the run or refreshing the page.
However, one thing to note is that passive scaling sources, whether it be archangel armor's haste application or stopwatch's damage scaling are almost always able to outspeed natural turn-based scaling by a fair margin (assuming you actually know what you're doing), as long as the enemy can't poison you. As anyone who has tried to tank snake poison on endless mode has known firsthand, once the poison numbers exceed your maximum HP, you're just dead. :)