1. look briefly through something or remind yourself of information (usually not for the first time)
run over notes/plans/instructions
'Run over' is a versatile phrasal verb with a number of meanings. In this meaning, we use it to talk about briefly reading through something (again) or taking a closer look at something to remind yourself of the details. People can 'run over' their notes for an exam, or their plans for a presentation, or the set-up instructions for their new laptop. There are lots of possibilities. You can use 'run over' in any context.
2. continue or end later than expected or planned
run over by 10 minutes, run way over time
If something 'runs over', it doesn't finish when expected. Meetings, classes, or appointments of any kind can all run over; and you can say how long they ran over by adding the preposition 'by' - "The class ran over by 10 minutes" - or by just using the word 'time' - "The meeting ran over time and I'll be late home". You can use this phrasal verb in any context, social or professional.
3. hit or drive over someone or something in a vehicle
I ran over a dog/cat with my car
This is very similar to 'run (sb/sth) down', where it involves hitting something with a vehicle. It sounds like it literally means driving over something, and that is generally when it is used. Unlike saying 'I knocked someone down' or 'I knocked someone off their bike' when driving, 'running over' something is more likely to be used in relation to animals or something small on the road. However, it can be used if something big drove over a person or a bike.