While exploring, one time in the Nightfall Bandit Camp and one time in the Nightfall Dungeon, I have encountered a wooden crate and chosen to leave it alone. When I continued exploring, the crate appeared again and I ignored it again. Then, the game starts telling me, "You have encountered an enemy!" but instead shows a crate when I continue. The first time this happened, I finally opened the crate and the exploration continued as normal. The second time it happened, I eventually encountered a chest instead of a crate and opened it. The graphic on the opened chest screen was a wooden crate, but it seemed to behave like a chest anyway, and then the exploration continued as normal.

edit: Happened again, seems to happen every time i ignore a wooden crate event.

@Effigy

I believe I fixed it. Let me know if you (or anyone else) has any other issues like this. Sorry!