I have currently been taking the birth control marlissa for 5 months and have brown spotting/discharge after sex/masturbation and a few times will see an old clot being passed when i urinate. what could this mean?

Breakthrough bleed: Sounds like breakthrough bleeding which occurs when you have bleeding at unscheduled times while on the pill. Brown is simply old blood that has been sitting at the back of the vagina. Often things get back to normal the next cycle. If not then schedule a visit to discuss changing brands or changing birth control methods. This is very common. Other than being annoying it is not dangerous.