I have a 360 GLT with a spoiler. After it has been standing in the rain for a while, when I open the hatch water pours out from inside the door, one of the black plastic stoppers is missing on the left side, water comes out of this.

My guess is the water gets in under the spoiler and enters the door though there. If it was parked on a flat surface it would probably drain out through a hole in the centre bottom of the door.

Just clean it out and stuff it up with silicone? Or some other solution?

I have the same problem. I removed one of the black plastic covers on purpose because I noticed that there's water inside.