Hi there. At the outset, one would require a more detailed history to make a clinical diagnosis & more so on the net. Is she sexually active? when was the last sexual contact? unprotected? Were her periods hitherto regular? If here periods are 2 weeks late, when did the brown discharge start? what pregnancy
test was done exactly? Was it on the blood or urine? I would recommend doing a serum/blood B-HcG
test that will give you a clear picture & a titre to boot. It is possible she has had a 'spontaneous' abortion
. Did she take any pills post coitus? For the moment, your friend seems fine. If she is pregnant or not, will be answered more definitively after that Bhcg test. Protein in the urine can be a normal occurence or occur with certain dietary intakes.
Do hope all well & wish both you & your friend continued good health. Do let us know how things pan out & hope all works out well. Cheers!