I have an X-Pro2 and X100S. Compared to the X100S, the X-Pro2 gets much warmer, especially on the bottom plate and the screen. I was initially worried about this and acquired another new X-Pro2 for comparison. I ran an informal test by leaving both X-Pro2 units on for an hour with the screen running. Both X-Pro2s got similarly warm. They were not hot or overheating, but noticeably warm.
I also did this test comparing aftermarket Wasabi batteries with the OEM and saw negligible difference.
Another X-Pro2 user also told me his camera gets warm. So, the warming seems to be normal or at least common. To be fair, I don't notice it much while out shooting, but I usually have the leather half case on.
Let me know if anyone here has more information to add. Hopefully this isn't a problem.