9 week old - problems while breastfeeding

Hi everyone. My 9 week old daughter has been doing some weird things while breastfeeding that started this past week. Every once in awhile she will actually cry while on the breast. I think she is now doing it more frequently though. In addition, she is squirming and pulling a lot after the first few minutes. Has anyone experienced this? It isn't during letdown so it's not that she's having a hard time with that. She only has one bottle a day with the exception on this past week because my husband has the flu, so it's not like most of her meals aren't at the breast anyway... it's to the point where it's getting uncomfortable and I'm not sure what's happening.