John is shown wearing Homer's old bowling shirt from the episode "Team Homer." At the end of that episode, that shirt was torn to shreds by one of Burns's hounds.
Homer's black eye and bruises disappear by the final scene.
When Marge tells Homer John is gay, Lisa is present and the three are eating breakfast in the pajamas. In the next shot (following the commercial break), the three are still eating breakfast, but are now in their normal attire.
When Homer, Moe, and Barney are leaving the sporting goods store and Homer sees his family in John's shop. Homer's arms are full of supplies here, but these supplies disappear when Homer starts to tell Marge that he's taking Bart hunting.
John points out the plumbing supply store where Lupe Velez bought the toilet in which she drowned. Velez's death by drowning is an urban legend with no basis in fact. Its origin is generally attributed to the book "Hollywood Babylon" by Kenneth Anger.