I was just doing the sand tentacle boss with a group, and it wouldn't let me walk back in after being defeated. When I entered the dungeon, the gate was down, and of course it wouldn't let me port to anyone. This is so frustrating. Then because I couldn't get back, everyone else died too. What a colossal waste of time.
Sometimes, if the realm you are on is full, you will be sent to a less crowded realm after defeat. When this happens it resets the dungeon.
From the Player Guide: "Dungeons must be completed to get full credit. Logging out, leaving through the Dungeon entrance, going to another dungeon, playing a Mini-game, going to a PvP or Derby match, or going to your home will reset the Dungeon. Leaving any other way gives you 30 minutes to return before the Dungeon resets."
While returning to the dungeon sigils after a defeat or port allows you 30 mins to return before resetting and does work most of the time, I wouldn't consider it a "true" strategy. The intended goal is to defeat the dungeon in one fell swoop. Wizard101Central and Mercenaries101 websites have strategies to help accomplish this.
Never seen this happen, but in the Aquila dungeons you can and should mark a spot. You can always port back in that way unless you are gone for too long. The only reason I can think that you entered another instance of the dungeon is that you changed realms. You can't do that and walk back in. Not a bug.