My Fit has been driving me crazy with water building up in the trunk/spare tire well. I finally dug out the hose and sprayed the rear hatch from every direction, eventually getting under the car and spraying upwards. In short, I think I found some leak-prone areas.

• There's a wiring harness coming in to the spare tire well on the passenger side. It wasn't fully seated and leaked water like crazy. I took the bumper off, removed the grommet, smeared some Honda Bond around, and re-seated it. Since this harness is for the smart entry sensor and beeper, trims without push-button start likely won't have this problem.
  
  
  
• The four bolt holes for the rear bumper also let a good amount of water in. It's important to note, my bumper was removed and these holes were empty. I don't think they would leak nearly as bad if the bolts were in place, but it's something to keep an eye out for. Loose/missing bolts might cause a leak.
  
  

There are many accounts of GD/GE Fits leaking from the roof so I assumed that would be my issue too, but it wasn't the case. I hope this info helps someone, or better yet hopefully your trunk never leaks to begin with 🤞