Happening again. 4 people went into the Great Spyre for a Malistaire run, one ported out as bait, and cannot come back in. No one else came into the dungeon.
Don't have an answer but I have experienced a similar issue: One time we went in with 4 people on the sigil. Someone ported out and back, then we were cross porting to hit the crystals and we ended up in 2 different full dungeons!
Some dungeons/instances don't allow anybody to teleport in.
As for those that do allow this, sometimes another player will teleport in to a friend, which fills the dungeon again. Also, sometimes the server simply hasn't updated to realize that you're gone, so it will list it as full until it updates.