The cadaver that Lucy was too familiar with was on the table in the first episode of the show. As the "cadaver" looks not frozen, it would have been decomposing (at least internally) by then.
Before the appendectomy they all do not wear their surgical masks properly. When Turk starts the operation he touches his mask in order to put it on with his sterile gloves on, which would make his hands unsterile.
In the final scene, Lucy finds J.D. who is playing hide and seek with Turk. After he hides again, Turk enters and says "If J.D. sees me, tell him I wasn't here" when obviously, he should have said "If you see J.D." or "If J.D. asks you".