Exactly. That is probably what you were seeing. If you zoom in all the way, I believe you can actually see the effect of them being phased out.
More information on PT though.. It is an ability found on hangar platforms of the Vasari and is in the fourth tier of the defense tree I believe. When activated, it drains massive amounts of AM, but it also negates an infinite amount of SC. It is so powerful that many Vasari players have built hangars without squads so that all their AM can go to pumping out this ability. This let's the Vasari ignore strikecraft when on the defensive and a Kortul lets the immunity follow your fleet through one of its abilities called Jam Weapons.
On a side note, does PT allow SC to be damaged from lack of a carrier? Let's say you stop the SC, and then kill the carrier. Could they potentially die while phased out? Just curious...