Overrun is a verb.
It can mean to spread over or occupy (a place) in large numbers.
For example: If bin collections do not improve we could be overrun by rats.
It can also mean, to conquer or occupy a territory by force.
For example: The enemy had overrun the country during the first half of the war.
Run over is a phrasal verb.
It can mean to collide with, knock down, and even physically go over someone or something.
For example: The child was run over by the car.
It can also mean to go beyond a time limit.
For example: Presentations would often run over due to bad moderating.