If something was running around on your roof at night, it wasn't squirrels. Rats, cats, raccoons...but squirrels go sleepybye at dusk.
Far as critters in the house go...I put a cat door in the basement of my last house. One morning about 2 AM, the cat jumped on the bed to wake me up. It seemed pretty obvious she wanted me to follow her, kinda like a feline Lassie, so out to the front of the house we went. Three juvenile racoons digging in the trash in the kitchen. The cat sat down and looked at me like "they're not MY friends".
I propped open the front screen door and chased two of them out with a broom, but one ran the other way, to the back of the house. Try as I might I couldn't get it to go out the door. I finally cornered it in the bathroom, and shut it in.
I went and got my fire tongs, then caught the thing by the neck, and dragged it out the front door. Needless to say, the cat door stayed locked after that.