What's wrong to mix jQuery with http://ift.tt/1DLGgkX?

I came from backend dev to frontend dev just recently, so I'm a totally newbie here and having a lot troubles cleaning my head up.

One of the problems is that I was trying to integrate twitter-bootstrap-3 with one of the mvvm frameworks naming backbone.js, angular.js and ember.js. I was really confused to see some repos in GH trying to rewrite some js part of bootstrap. What's wrong with jQuery in these frameworks? Would it be wrong to mix jQuery code into these frameworks? Thanks a lot!