Hello, I Had Sexual Intercourse With My Girlfriend, She Is

Hello, I had sexual intercourse with my girlfriend, she is on birth control ( not exactly sure if it works because sometimes her cycle does not match the chart, even though she has been on it for about 6 months) I used a condom and ejaculated in the comdom ( out side of her) I took off the condom, waited about 20 mins then rubbed my penis with my hand and tried to remove pre - ejaculate, I stuck it in her without protection for 2-5 mins, then put a condom on and had sexual intercourse again, and ejaculated out side of her, the next day within 24 hours she took a "morning after pill" and about a week or two later ( yesterday 2/1/16) she had a brown discharge... Is this normal? She has taken the morning after pill before and has not had a brown discharge, today 2/2/16 she has a tampon in and had a very light blood flow on it, do you think she is pregnant? Is this brown discharge normal? With the information above what would you say the chances of her getting pregnant are? also you should know she has only had one partner and has never been ejaculated into. Thank you.