It is actually the discharge that determines your cycle count. You charged it 3 times at 65% each, which means it was discharged from 100% 1.95 times. Then consider the discharge when you got the phone and the discharge after your last charge and that could easily leave you with a cycle count of 3.
Consider the example provided by Apple here. If you charged the phone 75% one day, and then the next day it discharged by 25%, it would then be 1 cycle count even without a further charge.
Batteries - Why Lithium-ion? - Apple (UK)