Is there any reason why when your stomach doesn't feel good, it puts you in a bad mood and you don't feel good overall? you feel annoyed.

That's all it takes?: We are all different in how we respond to adverse events--in your case, stomach aches. You don't have to feel annoyed or in a bad mood during these, or other, situations--it's your choice. Nobody feels perfect all the time, so modify your expectations of your body, ; take the opportunity to develop a tolerant, adaptive response when transient perturbations in your comfort arise.