Amoxicillin side effects

My 2.5 yr old is taking this for the 3rd time in 2 years, for an ear infection. We noticed no side effects with the first 2 times. But half way thru this medication, 2 nights ago, she started crying, rubbing her eyes, her ears, or nose, her stomach. It starts only at night about 30 minuted after taking the medicine and lasts nearly 2 hours before she will finally go to bed. I just put 2 n 2 together that it might be happening bc of the medicine bc this behavior is out of left field.

Is this an actual side effects some toddlers get with this medicine? Why is it happening at night and not during her AM dose??