I've seen 1 inside the park HR in 100+ games played out. I'm pretty sure there's not an issue there
As mentioned, I'd guess there's some sort of settings issue, perhaps, if you're seeing a lot of them.
As for the mismatched animations, we're watching from a very highly zoomed out perspective.
There are plenty of reasons a player could appear to arrive soon and be called out or vice-versa. I just watched a play in the real-life Diamondbacks-Giants game where Blanco was called safe on a steal of second but then ruled out because he was tagged in between his front and back foot hitting the bag, for about 1/10th of a second neither foot was on the bag despite his clearly beating the throw, and it was only visible in super slow-mo reply.
That would've looked wrong in 3d in OOTP. A lot of what we're seeing in-game can be explained by similar stuff.
Which isn't to say that nothing's wrong with how the animations match up. For sure some stuff does look weird and isn't totally right. There's plenty to fine-tune there, and Matt's definitely looking at all of that and working on it!