Once it is sandwiched and quilted it should be ok, as long as no seams are actually coming apart. You don’t have to do extreme dense quilting but do follow the minimum requirements for the chosen batting. A cross hatch in straight lines, or even gently wavy lines will probably take any stress off your seams..
I always starch my fabric before cutting, it helps with nice accurate cuts and does cut down on excessive fraying. But it’s too late now. Unless you have very light fabrics with dark threads showing through I wouldn’t worry too much about clipping them.