By design you can only enter the Temple of Doom once. If you have the Developer's Cut version of the game, you can head to the bandit camp, then use the Developer Mode cheat window (F11) to unlock the door.
For D2:ED/DKS, if you left the battle tower using the teleporter shrine and have not used the dragon stone again, try going back to the tower using a teleporter shrine and then use the dragon stone to 'leave battle tower'.
If that doesn't help, do you have a save either before entering, or before leaving?