It's possible that your body is "getting used to" the birth control. If you haven't been on it long there is a chance it is just your body still adjusting to it. You are taking hormones, they are bound to screw with your cycle for a bit. When I first went on the mini pill I had a period that lasted a few months! Now I'm on the implant I hardly ever get periods.
Hormonal contraception will most likely affect your periods - the combined pill will actually regulate them. You don't have a natural period on the combined pill, and many mini-pills actually stop your periods or can make them irregular.
Stress can also affect your periods, as can sudden weight gain or loss.
The best way to know is to take a test. It is too early yet to test, you need to wait until two weeks after the unprotected sex, as then if you are pregnant the hormone will be at higher levels in your body and will be detectable by the test. If you test too early, you will most likely get a false negative result. Also you would not be showing symptoms of pregnancy yet, you do not normally get these until about two or three weeks down the line.
If you are on the pill, you are protected after a week of taking it. If you miss a pill, what you should do depends on the type of pill. With most pills you should use condoms for a week after your missed pill if you have sex. How long after missing your pill did you have sex?
If you are spotting and producing discharge which is smelly then it is more likely you have an infection.
Book an appointment asap with your doctor and tell them your worries. They can carry out a pregnancy test for you, and also obviously check for infections.
Also for future reference, just in case you don't already know, there is emergency contraception for just this sort of situation. The emergency contraceptive pill is available over the counter or on prescription, and will prevent pregancy from unprotected or risky sex for up to three days (72 hours) after unprotected sex. It is much more effective the sooner you take it.