A condom stops working when it either breaks, falls off, or gets a hole in it. Unless this woman is running a mill out of her basement to create condoms that have been infected with stds, I think you should be okay...Assuming the condom remained intact. But, by all means, use this as a lesson to carry your own condoms - for all you know, she may have poked a hole in the condom before giving it to you, and this would increase your chance for contracting venereal diseases as well as impregnating her.
If you are very worried about this, you can get tested. The current symptoms you're experiencing could be the result of many things, but stomach problems are not signs of an std, as far as I know.