OK I'm 21 years old and I thought I had a vaginal infection so I used an over the counter vaginal cream to treat myself... during treatment my period came (its irregular) so I stopped using the cream. When I thought my period had finished I continued using the cream then my boyfriend and I resumed sexual activities still I thought all was well... then I noticed that my vaginal discharge turned dark brown (eww) for about 3 days now.. so could this be my body cleaning itself from the extra cream and blood that was probably still there? This situation is so scary need advice!!

That was the rest of your menstrual blood. You should continue the vaginal infection treatment if you need to.