1) what is the methotrexate being taken for?
2) How long have they been on methotrexate?
3) Is the prescribing Doctor a rheumatologist or a general practitioner?
4) as asked before, what is the amoxicillin being used to treat?
If the methotrexate is for any of the rheumatic conditions (SLE, GCA, RA, Sjogrens, PMR), school of thought varies. If patient has been taking mtx for along time (lets arbitrarily say for 6 months to 1 year) and has not had side effects, and has been taking their folic acid appropriately, there is a slim chance to a mtx side effect will happen. (yes the risk is there, but as long as the pt is on methotrexate, they will always be at risk for the random hepatic tox associated with methotrexate)
People on chronic methotrexate for rheumatic conditions are susceptible to infections, so having an acute infection during treatment is possible. In this day and age of everyone being "allergic" to penicillin, and many doctors throwing an oral broad spectrum antibiotic at the slightest sign of infection (due to resistance and/or unclear bug so throw empiric at it), having someone that could be helped by penicillin would be refreshingly amazing. I digress.
Methotrexate maintenance is usually once a week, with prophylactic folic acid 1 mg daily (except day of methotrexate). A prescribing Dr. has two options. either stop methotrexate for 1 dose, or just continue on. If a true infection is suspected, mtx should be stopped until S&S are cleared/ antibiotic tx is completed since mtx if being counterproductive. If S&S are very mild, and/or patient's rheumatic condition has had a history of being very volatile, maybe that methotrexate would make all the difference. Considering the biologic half life of methotrexate (not just the PK half life), the true benefit of stopping that 1 dose to avoid a potential ADE remains to be discussed.
Why I asked if prescriber is Rheumatologist or a GP: Rheumatologist (ideally) know their anti-rheumatic drugs. If not, they would be a bad thing. A GOOD rheumatologist would have a follow up appointment(s) with the pt. A GP, its very variable. they could have a good knowledge from lots of pts on mtx, or just as much as their POS ePocrates.
For methotrexate tox, I'd be more worried about chronic toxicity of the liver and bone marrow supression (hence folic acid scavenger). Poor Renal clearance would predispose patients to the liver tox and marrow supression. At that point, hydroxychloroquine and/or leflunomide are considered. (not counting the battery of biologics available).
Sorry for the long winded response.
anyone interested in rheumatology: two volume Kelley's Text book of Rheumatology and/or Primer on the Rheumatic diseases are nifty starter references without having to dig through pubmed. Only got to read parts of each when I rotated with rheumatologists.