Although your post is not detailed enough for me to be able to know where this issue is precisely, I had an MRI Enterography done a few years ago which showed inflammation and bowel thickening in the area at and above the J Pouch inlet. This is not uncommon and can be from backwash stool/SIBO in the neoterminal ileum due to the lack of a backsplash valve in the Pouch. In addition to this my J Pouch inlet is also narrowed due to inflammation which shows up as a thickened bowel wall.
Doctors have problems discerning whether this issue is Crohn’s Disease or just SIBO and pouchitis due to an inherent mechanical problem in all J Pouches (no backsplash valve). The actual or correct diagnosis is irrelevant; it’s bowel inflammation, and either way it has to be treated. All treatments for bowel inflammation in that area are the same. It’s how you respond to them which varies with the individual.