We also have a 3100 but only had water in any storage compartment if I didn't latch it well. The ones with two latches will leak if both are not latched.
The one you are talking about only has one latch, the lock. Check your gasket by putting strips of paper where the door meets the gasket, lock it, then pull out the strips. They will pull out easily if the seal is not tight.
Considering the age of your 3100, it would not be a surprise to find the gasket is compressed and no longer fills the gap.
2011 Sunseeker 3100
2016 Ford Edge Toad