My 3 year old son is half way through antibiotic course for tonsilitis and woke up with sore lower legs. was very painful in morning then before bed?

Was strep test done?: Antibiotics are only needed in tonsillitis if it is strep. Viruses are a very common cause of tonsillitis & many will have sore muscles as a common added symptom. Flu B often produces a classical picture of pain in both calves bad enough they won't walk. I doubt this has anything to do with the antibiotic but a call to the kids doc would be reasonable.