I've been a Stooge fan for exactly 30 years (after receiving Moe's autobiography as a present in 1979), and I've never seen any outtake footage from their shorts.
I've seen stills of deleted scenes ("Three Little Pigskins," "Malice in the Palace"), and I think that's about as close as we'll ever get. Columbia wasn't exactly Poverty Row, but they were close, and they didn't have the resources to save, store, and catalog discarded footage. Possibly they saved outtakes from some of their big budget feature films but certainly not from their shorts department.