Pilot Archive

Was doing duty missions yesterday and on few occasions I noticed that I was hitting an NPC ship when I wasn't supposed to hit. This happend when an NPC ship was very close and above (or below) me and I was still shooting and before CU I wasn't supposed to hit it but this time I was....
Something tells me that the 'hit-boxes' got shifted from their original positions not only for capital ships but for all ships... Can anyone confirm this?