There are also some phrasal verbs that go with these prepositions that don't always follow clear rules. For example to "come at" somebody means to attack them [He came at me with a knife.], but to "come on" means "hurry" [Come on, we are going to be late!] and "come onto" somebody means to flirt with them [ He came onto me at the bar]. You can find some phrasal verb dictionaries online that will help. https://www.englishclub.com/vocabulary/phrasal-verbs-list.htm

Each applies to a location reference point. "In" is always 'inside of' or 'contained within' "On" is always 'on top of' or 'over' "At" is always 'nearby' or 'in the same area' The applications vary because many can apply to multiple situations involving any number of different objects or locations. For example, you read what is written IN a book, but you are reading words that are ON the page.