I have had this happen with W&N batting when I loaded it upside down. When I cut and flipped the batting it was fine. I always check underneath after the first 12 to 14" of stitching to make sure nothing is going wrong on the backside. Then I check with every advance and every bobbin change. I have had tension go off because a blob of lint got stuck in the bobbin spring mid row so that is why I check early and check often. Usually with every advance.
In your case I would bet the batting was W&N and it was loaded wrong way up.
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Other things that could cause this is a dull needle or it had a burr on the end which pushed pokies of batting through. Unfortunately nothing will correct the problem. You can camoflauge it by taking a black permanent marker to the pokies. Washing will sometimes get it to draw up but it won't make them disappear entirely. The only real solution is not a pretty one. Either rip the entire thing out or completely "skin" the quilt (which will sacrifice your backing), and start over. I am sorry you had to experience it. Pretty much every longarm quilter will at some point in their quilting journey.