Understanding bilge

[Abbeysdad]

I made a point to run the bilge pump on the last leg to the dock and I know it pumped dry. But when I got home and pulled the plug, a fair amount (like a gallon or two) of water came pouring out. Now I didn't take on any water on the deck and the only point of entry I can see is the access panel (over the bilge pump) in the rear just ahead of the transom (e.g if I slow quickly and the seal is bad).
I'm wondering if the water getting in here or perhaps somewhere else, and can it get trapped up front somehow?
Advice appreciated on what I should do, if anything.