Firstly, brown discharge after your period is normal. You didn't say at what point in your cycle you noticed the fresh blood you have experienced, if this is mid cycle, it could be due to ovulation (egg releasing). Some women may experience mild pains and can also spot a little at ovulation time.
Intercourse shouldn't be painful and is something that should be investigated. If you have only very recently become sexually active, then it may be understandable. Make sure there is enough lubrication before penetration, if you are dry when he enters, it could cause a small tear and make be the reason for a bleed.....and the discomfort.
If you have been sexually active for sometime and the pain is deep inside your pelvis, then it may be worth asking a doctors advise.
Hope this helps