Dull rotary cutters are no good, that's for sure. I'd suggest you change the blade.
It looks like you didn't square up some of your HSTs and as a result some of them are oversized. In that case, nothing will line up and it is no wonder that you are frustrated. I always sew my HSTs and QSTs oversided and square them up. It may be more prep work but MUCH LESS headache in the long run.