What kind of windows did they install...whole new frames or "pocket replacement" windows?
If you don't have new sills and frames...they are pocket replacement windows and all that was taken off to remove them was the strip of trim right next to the new window sashs on the inside. If that is the case, simply remove that strip of trim, and get some non-expanding foam insulation and fill that gap behind there. Use some masking tape to keep foam from sticking to the finish surfaces.
You can stuff in fibreglass, but it doesn't seal as well as the foam. Be prepared to use up the whole can (s) of foam...there is probably some gap or crack somewhere in the house that can use the excess. Or find those guys that installed 'em without insulation and...