I have had that happen and found that sometimes the sewing machine needle would hit a seed and would make a skipped stitch. So taking them out is a good solution.
I also will sewing smaller pieces of batting together to make the size I need. You can't tell that you have done that once all the quilting is done. I always cringe when I see people throwing away large long strips of batting that the have been cut off the edge of their quilt in the garbage.