Initially I prewashed everything. Now I usually just do flannels as they can have such different rates of shrinkage from one piece to the next. So most of my quilts have both prewashed and not prewashed in them. I'm not aware of any major problems as a result.
Where my problems occur are due to either failure to square up before stitching to next section or scant 1/4" getting too scant for whatever reason.