I didn't see this in a quick perusal of the bug list in 1.1... I am seeing a lot of cases where I literally cannot find or see some of the enemy ships in command view. I don't think I am just missing them, as I am in some cases pointing my ship straight at them in the game view, then switching to command view and then lining up the view in that as well to the same orientation and viola, there is no red dot in front of my ship.

Not a real big deal but might get annoying when fleet commanding. Is this something already reported or something that only I am seeing?

Bueller? Bueller?

Could it be that the ships are outside your sensors (radar ....) range?

Most likely you are talking about the mission markers. Currently the mission markers do not display in the command interface, which I will fix sometime!

Once you get within sensor range, the mission marker will change to a target box / icon, and this should always be visible in the command interface. So until you pick them up on sensors, they will not be visible in CI.

Keep in mind that sensors are down in cruise mode, so you won't have much luck finding them in the command interface in cruise!