There is something wrong for sure, the windmill should not be occupiable after destruction, anyway.
As for the destruction animation, I've made a comparison video about it here:
Windmill destruction animation comparison - COH1 vs. COH2
Ha. So I was right, it was nostalgia. And this makes it even worse, its just a failed copy paste and not even updated. There are a lot of these buildings in the builder that are entirely bugged, there's a few that even have campaign hardcoded units tied to them.
But again, this isn't related to the 64 bit patch. This has been broken/bugged since CoH 2 launched.