A wizard did it.
The shopkeeper did it. In fact, the shopkeeper is probably Indie's rival. He's got a mob of yetis, cavemen and cultists out to kill our spelunking hero, all the while trying to make a buck by selling Indie stuff. Why else would he be kidnapping damsals to put in kissing booths? To spite Spelunky man and make him attack, so Shopkeep can kill him without looking like a bad guy.
Also, the shopkeeper has mastered ninjutsu which is how he appears to be in many places at once. The last shopkeep you kill before exiting a level is the 'original', and he always come back from the dead. At worst, he suffers major-burns or lead in his face, and at worst, falls down a pit or lands on spikes. Maybe he keeps coming back?