I have this issue with my 2014 (one of the back doors), but not with my 2017. It's not a big deal with mine, I shut that door with a little extra effort or it shuts normally with windows open.
I've had this issue with my 2014 Limited since I bought it new. The dealer told me that it wasn't covered by warranty. I noticed it the first time I washed it. I figured since it was new they'd do something about it, but I was told to take it to a body shop. Now I just ignore it.
I bought my first 4Runner in 2014, a Limited. My wife also love the truck and it fit well into our lifestyle and New England weather. This year we pulled the trigger on a 2017 TRDP for me and she's fulltime in the Limited now. We're both very happy with the decision.
I've bought many cars/trucks in my life and Falmouth Toyota is by far the best dealer I've ever dealt with. Not only is buying a car there a walk in the part, but the service department is has never screwed me. I hate service departments way more than sales guys.
Ended up with Toyota liners for the front and rear, and then went with Husky cargo liner. I have the standard Toyota all weather floor mats and a Weathertech cargo liner in my 2014 limited and I like the setup in the new 4Runner much more.