I've got two thoughts.. or more..
First your description says not enough humidity.. for pupating.. As an avid hatcher of chicks, ambient humidity counts not just intake.. are the pupa drying out?? Moisture for hydration is not the same as survival. When they can't fully molt, they're deformed and never perform well.
Second thought.. too inbred.. pick out EVERY one of the meal worms
that is deformed.. deformity breeds forward in too many instances for this to not be factored in.
I didn't know that microwaves heat moisture!
I have used the microwave.. which did make my wheat hot as heck.. but if left to sit while cooling off.. would clump together where the moisture was.. I keep my wheat in air tight storage.. after ditching the SLOW turn around (due to my temperature) adventure.. I later found ALL the wheat left in my "air tight" container.. in fact mildewed! I had not expected that.. I thought maybe rancidness would be in question.. but there's no mistaken that mold smell. What a waste and a bummer.
I wonder if it would not have molded if not in the enclosed container or if that was it's fate? What seems dry to us still does have a percentage of moisture.
My birds eat the dying or dead black worms as well.. dried out beetles or pupa, oh ya..
I set my veggies on top of folded newspaper that covers the surface of substrate. Celery and cabbage leaves works well for me to avoid any mold issues. Even broccoli stocks.
A couple links that might have helpful information..
Live Mealworm Information
mealworms