This is a very strange bug having to do with the 'white bracket' hotkeys list. If a wing of hostile fighters jumps in after the mission begins, those ships will not appear with white brackets when the proper hotkey is pressed, even if they were assigned to be in the list for that hotkey.
Me and FSF have been troubleshooting the issue and FSF came up with the specific scenario where it breaks. You should be able to target both hostile wings in white brackets by pressing F12, but you are only able to target designated fighters from the first wing, the wing that was in the mission area when it began.
http://www.mediafire.com/?gzcgwd7543337bvI would like to know if there is a way to fix this issue or some possible workaround for it. If there is a way to 'trick' FRED into doing the right thing I am all up for that as well.