I've been on cerazette for around a year now and at first I got a little worried that I might be pregnant because like you've described i didn't have a proper period, just some brown stuff.
I took a pregnancy test and it came back negative, I also spoke to my local family planning nurse who confirmed that period irregularity and the brown stuff were normal when you first start taking cerazette.
Now my periods have all but disappeared (the brown discharge returns once in a while and i've had one period which caused a lot of cramps and lower back pain) and I ensure I take a pregnancy test once every three months (when I pick up my pill I also request a pregnancy test) just to be sure.
I've missed a pill in the time I've been taking it and didn't fall pregnant. My advice would be to take a test just to put your mind at ease but don't worry too much because it's probably just your body getting used to the cerazette and adjusting to the fact it's slowly thinning your womb lining so that implantation is more difficult.