hello, i had unprotected sex 6 weeks ago and got the morning after pill within the 72 hours. i then experienced some bleeding  4 days after taking the morning after pill causing me to use a tampon. i went to the doctors and went on the contraceptive pill microgynon 11 days after unprotected sex and the same time i got checked out for any STI's. i tested positive for chlamydia and took a course of tablets to cure the infection. i then carried my pill over as i would have my period during my holiday. at this time i experienced brown/red discharge which startled me as i have never experienced this before. i took 2 pregnancy tests and both were negative, however the discharge has started to become more red in colour and is now looking like the end of my period. i am set to finish my pill pack in 2 days and i should get my period, i have experienced stomach cramps which are the same as when i would get my period. 
could this be because i carried my pill over and its just my bodies reaction to continuing with my pill or could this be a more serious matter. i am very concerned and a little embarrassed to tell my mother or friends to ask for advise. 

any advise or help would be greatly appreciated.