From what you said, though, your 'usual' was only for 2 months. Breakthrough bleeding is very common on birth control and can last a few months. It didn't just start, it started last month when you missed your pill.
It can take a few months for your birth control to regulate your hormones. It is important to take your pills at the same time every day as directed so your body can adjust.
Spotting after sex can be from an irritated cervix and is also completely normal. This may be what you have right now, a little cervical irritation.
Good luck!