I was doing the quest Den of Thieves for the Fighters Guild and went to Hrota Cave with Maglir and we both killed the bandits there. I returned to Anvil to drop some loot and to talk to Azzan. Then I immediately returned to the cave, both to get some other valuable loot that I couldn't carry and to get Newheim's Flagon that I forgot to pick up the first time. To my surprise, the cave was full of monsters.

I know that UESP wiki says that the cave is empty before the related quest and contains monsters when the quest is finished, but I thought it would be repopulated after 3 days, just like the rest. Has anyone else experienced the same thing? Just curious.

I haven't had the issue, but maybe you just cleared the area out right before a scheduled spawn.