The latex couldn't have hurt your stomach.

He was probably thrusting too deeply and hitting your cervix, which can feel like it's in your stomach.

Yeah, he was probably hitting your cervix, which feels like it's in your stomach when it hurts. Try having sex in a female-on-top position so you have more control. Then you can make sure he doesn't hit your cervix too hard.

If that's the case then that is likely also the cause of your spotting/bleeding and your cervix should heal within a few days.

But, if that's the first time you've used a condom it may be possible you have a latex allergy. It's not very common, and I don't know what an allergic reaction to a latex condom would be like, but you could get an allergy test to find out, and there are non-latex condoms available.