One can be allergic to pretty much anything, at any time.
As long it there is no itching/swelling, or the gastric upset isn't particularly awful, it's hard to say whether it's an allergy. And allergic reactions, unless ridiculously severe, shouldn't show symptoms immediately. If your mouth itched a few minutes after eating flax and then there stomach problems, I'd say yes.
Still, I'd avoid anything that makes you feel like shit.