The soft top is not great at sealing any of that out. And since all that is designed to come apart (to take the top off) it likes to do that on its own. But I would check the following, probably in this order-
1) Make sure both sides are latched down at the tailgate. I had a horrible whistle for a couple days and was shocked to realize that I hadn't fully latched the back end down. One good re-slam and we were good.
2) Check to make sure the corners are fully seated in the frame. The top corners have tabs that sit in the frame to kind of locate them on the frame. I would check that these are in there good. To do this, I would remove the side windows and check that the back window is in the center of the top. I would then make sure that the corners are seated. If not, I would give this a good thump. Some times it will pop back out and I readjust the rear window by moving it left or right in the frame and try it again. They both should stay in place, but it really takes the tension from the side windows to lock them in. I have had to do this procedure on my from time to time, mainly when I am moving between safari mode and all buttoned up.
3) When you reinstall the side windows, make sure that they are lined up where you want them- There is a lot of room to move these up or down and I kind of get OCD with this a bit.
4) I might check to make sure that there is nothing between the quarter panel and the lower half of the top thats keeping it from seating all the way. This is a bit of a long shot, but maybe? I am presuming there is quite a bit of adjustment in the top bows, so if something is cadywumpased there, you might be able to fiddle it out. I have messed around with some of the bits in the front, but not in the back, so I cant say for sure.
Final tip- I find that getting all this tight and positioned right in the back makes a differance with the wind noise, so I would spend some time getting the windows where I want them. I have found its easier to do all this with the front part of the top flipped back- it takes some of the tension out of the system and gives you a little bit easier time to work the adjustment.
All that said though, the soft top fitment is really my single least favorite thing about the Bronco. I love the functionality of the soft top, but you have to fiddle with it way more than you should, and even then, it still looks like a big floppy mess.
My solution to this involves turning up the heat and the radio until its warm enough outside to run a bikini top. Only like 3-4 months to go 👍
Good luck.
2023 Wildtrak. "Sometimes you got to get lost, to get found" -J Bronco