The crossbow in particular has had these issues since Dawnguard first came out, and they perpetuate in SE. The mods for first-person-only killmoves for classic Skyrim usually resolve the problem to some degree, but it won't fix misses. SE has no hope until we see SKSE for SE finished.
It seems to come from a "guess" made by the game when you fire a shot. If it would normally give a killmove for the shot, this triggers, but the game has to assume the kill or there'd be no move to display. That means, not calculating for falloff (since falloff for bolts and arrows in Skyrim is wildly unrealistic), your shot would probably have hit. Once the game imposed physics on the arrow, however, the shot actually misses.
This can happen in melee as well, if the weapon is particularly powerful or if something causes the target's ragdoll to react. This is most evident when using mods that break the enchantment rules; a 84 dmg dragonbone sword with 918dps/5 sec lightning will kill nearly everything in one swing, but if it's an opponent with immunity to shock damage, the killmove may happen only to allow the enemy to get up and fight back. This also happens in 3-party fights: if a Draugr Overlord uses Unrelenting Force or Disarm on your opponent while fighting them, you may enter a killmove only to be stuck because the target is no longer in front of you or has staggered below your swing, causing you to miss.