Nothing a revision wave wouldn't fix right? It would stink for the people that already bought the "first versions", but it's not out of the question.
Production runs change all the time, sometimes with minimal variation differences, sometimes with drastic ones. Toy Biz, Hasbro, NECA Mattel, etc. have had so many different production variants from their movie lines to comic/cartoon. Sometimes these consist of small paint variations to a completely different tool. It wouldn't surprise me if we see a revision of this Wave 1 TNBA Batman (along with Catwoman, Two-Face and Freeze) where the hip holes are non-existent and smoothed over like the shoulders,
especially if DCC has a problem with it too.
Like you stated, this is the perfect example that they're capable of changing the tooling of the joints.
With Wave 2 delayed and pushed back for next year, I could see Joker, Robin, Man-Bat and Ivy showing up free of hip holes. There will be a ton of Wave 1 produced, I'm sure if/when DCC smooths over the holes, Wave 1 gets revised in later batches too for consistency.