Deliberate mistake: Shawn fishes Mr. Feeny's watch from the septic tank and mentions the septic tank is deeper than it looked. Given this, he should be covered in human waste, instead of just looking a little dirty.
The Last Temptation of Cory - S3-E9
Deliberate mistake: When Cory calls Topanga from Missy's phone, he starts having a conversation with her as soon as he finishes dialing her number, with no time for the lines to connect.
Deliberate mistake: When Alan is trying to rush Amy out of the door, she yells from upstairs that she's still shaving her legs. A mere 20 seconds later, she comes downstairs wearing a dress and nylons. Even if she was for some reason shaving her legs while wearing a cocktail dress, that still wouldn't be enough time for her to clean off her legs, put nylons on and then walk downstairs.
Chosen answer: In the present day, with the United States abiding by more stricter school health laws, for the most part this wouldn't be in school cafeterias as many cannot even have carbonated beverage machines now. However, in the 90s when the show takes place, it wasn't unheard of for there to be coffee machines in the cafeteria of small schools where the teachers eat with the students as we see them do often in the show. The idea being that the cafeteria was small enough so a teacher or hall monitor could catch a student before they could drink the coffee.