A scupper is an opening in the side walls of an open-air structure, for purposes of draining water. They are usually placed at or near ground level, and allow rain or liquids to flow off the side of the open-air structure, instead of pooling within the walls.
Ships have scuppers at deck level, to allow for ocean or rainwater drain off. So on a raft it's between the floor and tubes. Terminology is not usually used with rafts but you get the idea.
There are some spots on the floor too that I have never been able to get rid of but I'm not worried about it.