Try removing your air dam in front of your wet/roof box, or spraying out the area under it REALLY well.
If you remove it, put the screws back in to seal the holes, and hose/wash it all out really well.
Mine often collected acorns up there. They roll down from the higher portion of the roof and get trapped... they are free to roll from side rail to side rail, and air dam to 2nd row... but can't get out.
The first time I cleaned mine (had owned it awhile) there was a whole eco-system up there. A little more, some soil from things breaking down, and tiny plants starting to grow in it, along with some small bugs.
This was what had collected a year after that. I no longer park under trees lol