Dear An: Gosh, breakthrough bleeding (BTB) can be a common side effect of most types of hormonal birth control (eg pills/patch/ring/shot/Mirena IUD). Among birth control pill users BTB frequently occurs after a missed or late pill. In your case it sounds like that may have been the case. More remotely, BTB in a pill user can arise if she has gotten a chlamydia infection. Yet, if you both are monogamous this is not going to apply.
When a woman uses hormonal birth control it can make the lining of the uterus more unstable--so it is easier to have some of it begin to shed. Sometimes the lining is less stable because the hormones make the lining much thinner (actually this is good as a thin lining is a healthy lining). A thin lining is easier to de-stabilize with elements such as a missed pill or heavy exercise. Sometimes the lining is unstable because the hormones can make parts of the lining out of synch.
As always, if you are sexually active, an undetected pregnancy should be ruled out.
In terms of the dark spotting, when the bleeding is brisk and heavy the blood flows quickly out of the uterus and vagina. When the bleeding is scant and slower it has a much longer time to be exposed to the oxygen in the air. This exposure will turn the blood color brownish. Think about a piece of meat which has been exposed to air for a while. The outside will be dark brown/gray. Yet when you cut into the meat, and expose an area which has not been in contact with the air, the color will be red.
It is very common for women using birth control pills (BCPs) to have a "period" which looks more like dark motor oil sludge than bright red menstrual bleeding. The synthetic progesterone in BCPs creates a thinner lining inside the uterus. This creates a decreased amount of flow. This more scant flow will appear as a dark brown color, and thick consistency.
In conclusion, if you are having continued erratic bleeding into the next pill pack, or the pelvic pain continues, you should contact your GYN. You are correct, sometimes one can skip a pill or so, and not have breakthrough bleeding--those women had good luck.
Yours,
Jane