I was taking amoxicillin 500mg for a tooth ache, i tested for gonnorhea and chlamydia 3 days into the treatment. results were negative but could the amoxicillin have caused a false negative?

Possible but unlikely. Amoxicillin is not reliable against either infection, but might work for some. More important, the test detects the organisms' nucleic acids (DNA, RNA), which persists a few days after the organisms are killed, and the test usually remains positive a few days even when treatment is effective. The bottom line is that it is very unlikely you had either one.

It would not against Chlamidia but may with GC