Irregular bleeding is a common side effect of the pill! Brown blood is normal on and off the pill, it’s just old oxidised blood (exposed to oxygen).
Skipping break weeks can often lead to experiencing side effects like irregular bleeding unfortunately.
Btw you do not have real natural periods on the pill, the pill completely stops periods. Any bleeding is a side effect of the pill, and can be anything from very very light spotting to very heavy bleeding, and light red to a very dark brown in colour.