In the archive footage Larry wears a vest; he is not wearing one in the new footage (except in one shot).
When the burglar leaves the house in the first half he's wearing a gray hat. When the boys catch up to him on the train he's wearing a white hat.
When Shemp's right leg is supposedly blown off in the explosion, it is clearly exposed when Moe and Larry carry him and Shemp quickly tries to cover it up.
When the Stooges spot the burglar on the train, Moe says "Hey, it's him!", but it is very obvious that the new line was poorly dubbed in because he almost says "Hey, it's Slipp!"