I noticed that when i was using a fleet of Generix Class dreadnaught refits to phase cloak through an asteroid field, when they were through and I ended phase cloak they were in yellow alert. I noticed this because they wouldn't attack on their own, as you know yellow alert is attack if the ship is being attacked. So only a few of them would fight. I decided to try and see if I could get it to happen again and it did. I do not think it is supposed to switch to yellow alert, that's why I think it's a bug. I discovered that as soon as you go into phase cloak it switches to yellow alert and stays that way unless you change it. This is easily reproduced, just build a generix class, refit it as a dreadnaught and research phase cloak. Then use it and it will switch to yellow alert. The screenshot isn't too good, but it does it's job.

Oh thanks, I never noticed before, I still think it should go back to red alert when you decloak.