maybe if you use tweezers? or is the quilt going to be washed when it is done? if so, the little bits would probably disappear then...i used to at times have that problem behind machine embroidered designs...i used tweezers, but found that washing usually fixed it for me...i spritzed with water on one project and took a wash cloth and (gently) rubbed,,,it worked without distorting an stitches.
if they are on the back and not noticable from the front you really dont' have to worry too much about it as long as it's just little bits it will be ok.