Maybe the water coming out is normal?
I was told by a great body repair guy, that the biggest problems come from people trying their hardest to seal water out completely. That is because of all the additional measures they put in place to seal water out will ultimately trap water in! If water gets in and can't escape, then that is when rust and rot happens.
Bad things can happen when people glob beads of silicone or other sealers completely surrounding any seams on body panels or accessories.
When I had this shop add fiberglass steps to my pickup truck, I tried to get this guy to seal all around the step to keep everything out. He insisted they only seal the top, front and rear edges of the steps where they contact the rocker panel. He said you have to keep the bottom edge open, so if the seal on top does fail over time (which they do)... Any water getting in from the top will be allowed to escape out the unsealed bottom edge for the step. That made complete sense, so that is how he did it for me. I saw similar trucks with the same steps getting rusty rocker panels after 5 years. Mine lasted almost ten years and still looked good when I sold the truck.
So maybe having the water pour out the sides is a good thing and supposed be that way... Draining instead of trapping.