The default cow, mooshroom, sheep, ocelot, etc. geo files are being seriously misinterpreted by blockbench. Am I opening them in the wrong format somehow? I thought perhaps they were reading them as java files, but I'm not sure.
#BlockBench misreads cow.geo.json
novel sierra
civic rock
Mojang uses a pre script to rotate that bone. So this is correct.
You can remove the pre script and make them look normal or you can edit them like this. Keep in mind the bone names matter.
I suggest making your own.
If you make changes you'll also have to in many cases make new animations.