This will happen if Ganon is not the dungeon boss and he sppears, you kill him once, then come back in a later playthrough, and leave the doors that open.

It's a rare occurrence, but there is a good example if you beat him in Lv. 11 of New Quest 2003 and 2013 of this.

When the videos of this go live in a couple of days on schedule I will link the timestamps.

Generally on the rare side, but can happen.

-James