I would also guess it's a virus because of the fever. But it is totally possible to get side effects well into treatment. My younger daughter can tolerate MTX for about 3 months. We have tried her on it 4 times, at 4 different doses. Around the 3-4 month mark, side effects become unbearable (she had nausea, dizziness, vomiting and fatigue). Before that, they're there but manageable.
There are options if the stomach symptoms (nausea, tummy pain) are caused by MTX. You can up folic acid - from 1 mg to 2 mg daily. You can add Zofran if he's not already taking it. If he is taking it, you can start giving him Zofran more than once.
You can try Leucovorin which is folinic acid and is used as a "rescue drug" when MTX is given at high doses for cancer treatment. For IBD or JSpA, a much lower dose of Leucovorin would be used and it helps a lot with side effects. It does make MTX less effective, so it is usually used with high doses of MTX - usually above 20 mg.