Do you have a pediatrician. If not, you might just call one, or the nurse at the children's hospital to find out. I wouldn't be alarmed by the crying as it probably hurts and the ointment, while applying it may irritate her soreness.
The antibiotic isn't oral right? If its just topical, I don't think that would cause a reaction. Double check the dosage for the amount of Tylenol you are to give. When my DD had high fever, I gave Tylenol and it made her feel better but she definitely seemed drowsy. Honestly, I viewed it more as a self-soothing attempt since she wasn't feeling good than a reaction to low dose infant Tylenol.