Is it like this?
If so then this is similar to a Humira injection site reaction. It's a little raised and itches. Do not scratch it because that only makes it bigger and more itchy. Try Benadryl if she can take it (always went away after I took 2 Benadryl at 25mg each). When I asked the pharmacists about it they suggested that I leave the syringe in for 5 more seconds to see if that helps to reduce the possibility of having a reaction (they said it was caused by the medication not clearing the needle entirely).
If this isn't the right image/reaction then contact the pharmacist and describe it to them (or show it to them if you can). They may have an answer for you. Hope she feels better.
Edit: When I got a reaction from Humira it took 1-2 days for a reaction to show. It's possible that a reaction for MTX could take longer or there was some other factor involved.