To 'run over' can mean for something to continue beyond an expected finishing time. If something 'runs over', it doesn't finish when expected. Meetings, classes, or appointments of any kind can all run over. So you can say "The meeting ran over so I'll be late home".
To 'run over someone or something' can also mean to drive over somebody or something in a vehicle. You might use this to say you 'ran over an animal' by accident on the road or you 'ran over a pothole in the road.'
To run over can also mean to 'repeat an explanation' so you might 'run over instruction's or 'run over an explanation' with someone. 'Run over' can also mean to read through something (again) or to take 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.
If something 'runs over' it can mean to exceed or go beyond the capacity of a container, if something runs over a cup or glass it spills because it is too full.
Additional examples with 'run over':
An employee is discussing expenses for a work trip with the accounting department.
"My expenses ran over the €150 per diem allowance, but I have kept all of my receipts."
A friend wakes up not feeling very well after a night of partying.
"I feel like I've been run over by a truck."