OPK confusion

Okay so ive been using OPKs for the last 3 months, and during my fertile window there is a faint second line, yes i know according to this they are negative, but during my not fertile window there is no second line.. What could cause this, and what can i do to help the lines get darker?? Ive never done temp before and not entirely sure how.. The kit i bought came with OPKs, HTPs, and a bbt thermometer.