Just noticed about a cup full of water in my carbon scott cr1, emptied it out via the seat tube.

How could it have got there? Have done a few rides in the rain and also washed it but can’t figure out where it could be ingressing.

And could it cause any damage (I know carbon doesn’t rust!)?

I wouldn’t be to worried, boats and stuff are made from carbon and they seem fine.

Empty it out and keep an eye on it, I would be looking more at the metal fittings in the carbon to make sure they are not rusting from inside.

Same with all bikes, just gets in at the top of the seat tube inside the seat clamp. There’s always a way in there!