The only time I had this happen to me was when my needle had leftover sticky gunk from sewing through some self-stick interfacing. And fortunately I could hear it was sewing funny so I didn't get too far before I corrected it.
Did you do the quilting on a long arm or on a domestic machine? I have heard this happens more with longarms because the needle is so much larger. I don't have a longarm myself though, so that's just what I've heard.
If possible, using a black batting if you have a dark backing might help at least disguise the issue.