Pills and spotting...please answer?

This is my second month on bc pills. The first month for me was fine, but this month I have had a lot of breakthrough bleeding. I know this is common in the first three months, but I was just wondering if it is safe to have while having some spotting? I have a little bit of spotting everday, and have talked to my doctor, who just told me to keep takin my medicine. Is my pill still protecting me from pregnancy during breakthrough bleeding, and is it safe to have (with condom too)?