It's completely possible for there to be an ear infection. Amoxicillan, though once a powerful antibiotic, has weakened over time as bacteria have become more resistant.
Our daughter (2) has had tubes twice. There's something about how her ears trap fluid, make a perfect breeding ground for infections, and it's us chasing the infections. She was great when the tubes were in place, but when they naturally came out, the first time, the process started all over again.
FYI - if there is still an infection present, stand protocol is amoxicillan, Augmentin (GI side effects common), Omnicef (red stools common) and then a consult with an Ear, Nose and Throat specialist.