What Causes Severe Throat Infection With Yellowish Phlegm After Augmentin?

Several months ago, I was diagnosed with hypothyroidism and prescribed Levothroid and Liothyronine SOD. Symptoms such as weight gain, heavy menstrual periods, fatigue, etc have all disappeared. This week, i got a sore throat with swollen tonsils and light yellow spots on tonsil and ear ache. I started taking Augmentin 875 for this. The ear ache is gone and the tonsil is somewhat smaller, but my throat hurts much worse, and I am spitting up dark yellow mucus accompanied by pain. Throat feels raw. I have only taken 4 doses of Augmentin. Am I just getting better very slowly or is Augmentin making it worse or is this somehow related to my thyroid? Please advise - your help is greatly appreciated.