Some people including myself can eat Jalapenos without getting diarrhea but it's normal for some people to get diarrhea when eating Jalapenos.
The reason that Jalapeno Peppers cause some people to have diarrhea is because of the capsaicin that Jalapenos contain which is not absorbed by the body during digestion.
The capsaicin in the Jalapeno peppers binds to and activates your TRPV1 receptors which irritates your stomach and can cause you to poop and have diarrhea.
So your stomach may not like the Jalapeno Peppers and then leads to diarrhea and stomach cramps.
The capsaicin that isn't absorbed by your body is another reason that your poop burns when it comes out after eating Jalapeno Peppers.