The short answer: Walt is supremely arrogant.
In much of the show, you can see that it is often very painful for Walt to treat others kindly. Walt is a brilliant guy, and he knows he is a brilliant guy. He also knows that most other people are much less than brilliant. Whenever Walt encounters a person that displays a lack of intelligence, he often can't help himself to a bit of grumbling.
In this scene, Jesse uses the word cowhouse. While it seems cowhouse is a word, most native English speakers would not know it. Native speakers would generally assume that Jesse is making up a word where most people would use the word "barn." It is likely that Jesse knows the word "barn" but, at this point in the show, a viewer would assume that either Jesse has fried his brain with drugs or he is so urbanized that words which belong to a rural setting don't come easily to him.
This is the basis of why Walt is annoyed, but the truth is actually more nuanced than this. Jesse and Walt have some shared past as Jesse had been Walt's student. In their respective roles, at least in Walt's mind, Walt was the brilliant teacher and Jesse was the disinterested student. He often treats Jesse as less than human because of this.
In any case, when Walt says "God help me", he is privately lamenting his fate that he has to work with such an inferior person as Jesse. To be honest though, in Walt's mind pretty much everyone is inferior to him.