Alright so I solved it for my case. When any of the verts end up clipping into each other and merge due to mirror mod when making the shape keys. The exporter throws that error. I fixed it by hunting down verts that merged during movement of the shape key and it fixed it. So not exactly an issue as it can be easily worked around. Just was confusing at first.

I might have narrowed it down to being a mirror modifier issue when using shape keys and they end up merging when they get too close. Disabling mirror lets it export normally. I will do a bit more testing to confirm if that's the true issue. I don't know if this is the same issue as the OP is having.

Same issue as well on my end. No matter if the poly count is 40k or 10k