there is no definite answer since there are multiple possible causes for this. It's impossible to tell without looking at the actual site, so please, share the link to your shop (preview link, if not published yet/has storefront password).
Well, the problem is the same -- the app you use ("QTY breaks") loads its own jQuery over the one used by theme. It breaks the theme code because the plugins added by theme to its own jQuery are no longer available.
Namely the theme add to cart code misses the prepareTransitions() in _showCartPopup function.