My son was dx with both Celiac and Crohn's's at the same time. He had been having stomach aches and eventually uncontrollable BM's.
We started with lab work that indicated Celiac. His tTG score came back at 72 and normal, or negative, is less than 3. Due to the lab work, his GI ordered scopes to confirm the Celiac. Crohn's wasn't even on my radar. Sort of the opposite of your situation. The scopes visually showed blunted villi and also lots of inflammation throughout. Biopsies came back confirming Celiac and also, much to my surprise, Crohn's.
We started the GF diet the afternoon of the scopes and had a brand new little boy three days later. Going gluten free kept the Crohn's at bay for almost three years. When the vomiting started we thought it was gluten, but unfortunately, it was the Crohn's finally making an appearance.
I would difinately ask if a Celiac panel has ever been run (and if not, request one) and also if they ever observed blunted villi during scopes. I've had one GI tell me you can't have both diseases, while another told me it's less than a 10% chance, and now our current GI is wondering if he was misdiagnosed and wants to do a gluten challenge. No thanks. If you want him tested, just expect mixed messages.
The symptoms of both diseases are identical except Crohn's sometimes adds a fever. We've had to be super strict with the GF diet just so we can rule out gluten whenever DS starts experiencing symptoms. I'd take Celiac over Crohn's in a heartbeat!
Good luck!