When fighting against enemies in very close quarters, 95% in V.A.T.S. is a sure miss. It's possible that this only happens when the enemy is on the ground level.
The game also has issues detecting obstacles in Vault-Tec Assisted Targeting System, it can show a positive percentage when the target is behind a pillar etc.
Example (it isn't possible to get a hit): https://onedrive.live.com/redir?resid=130B665BF39DFD1!4439&authkey=!AM6N_yIXHlIpeCI&v=3&ithint=photo%2Cpng