QD wool is thermal bonded so there isn't a right or wrong side to it. Typically I've found there are 2 reasons why a batting sheds on a quilt:
(1) the size of needle was too large for the thread or the size of the thread was too small for the flannel. I actually tend to use at least a size 40/2 thread (or 50/3) with flannel because the brushing tends to cause more spaces between the fibers. So if you switched threads or switched needles, that could well be part of the cause.
2) density of the fabric. All flannels are not alike. It depends on the width of the fibers & weight of fabric that they started with. Then it depends on whether it was brushed or double brushed, and what chemicals were added to the flannel. Some companies will pre-shrink the flannel before sale. Again, that process can vary greatly.
I often see recommendations to wash flannel in hot water and drying on high before quilting. I'm not sure where that idea came from. The brushing process already weakens the cotton fibers. Washing in hot water & then exposing it to more heat & agitation in the dryer will cause the cotton fibers to swell & develop microscopic cracks. Then it cools to room temperature (typically 50+ degrees F cooler) and shrinks back to normal size, but may cool in a bent position, making slightly more space for batting to come through.
At this point, I think the best option would be to use very careful laundering processes. A dye-free detergent, cold water (tap water cold, if your machine has that option), the gentlest cycle you have (mine has an intermittent hand wash cycle) in a top-loading washer to limit agitation. If possible, allow to drip dry a bit on a line before popping it in a cool dryer until 80-90% dry. Then remove & allow to air dry the rest of the way.
So, so sorry this happened to you. It can happen with any batting. The only way to ever be 100% sure it won't happen is to encase the batting before sewing -- but that's a huge hassle. I'd get one of those electric pill removers to make short work of the clean-up and probably do most of the "laundering" with a vacuum rather than in the wash.