When Lulu initially kidnaps Superman, she tears off the S logo from his cape to make her own costume. When he is later freed, the cape is repaired and restored with no time to change.
The corgi that was tied up next to Krypto disappears during Ace's "prison break" scene.
When Krypto and Ace talks about the farm (around 38:58) Krypto's right ear has some dents which disappear and reappear during that talk.