Shot question...

So I'm on the shot and have been for about 2 years, my bf and I just pull out instead of condoms. Well about 2 days ago he said he didnt quite make it in time and today I'm having brown discharge. I'm wondering if that's the shot killing the sperm? My friend is on the shot and let's her bf finish in her and I think I can let mine finish in me but hes more worried than I am. I get my shot exactly every 8 weeks so I trust it. Anyone else let their man finish in them on the shot?