In The Next Phase, they were invisible. Why couldn't Counselor Troi sense them?
We do not know, as Troi hasn't spoken anything during the episode
Well, as the heading says, according to Chakoteya, the only scripted response from Counsellor Troi is shaking her head, acknowledging that she cannot sense their presence.
PICARD: Mister Data, begin a level one diagnostic. All transporter systems offline until further notice. Could they have materialised somewhere else?
DATA: Negative, Captain. Sensors are unable to locate them anywhere within transporter range. PICARD: Counsellor?
(Troi shakes her head)
Additionally, from the screenplay (thanks to Valorum for the resource):
Troi waits a beat and silently "listens"... but her expression is grim. She shakes her head. That seems to seal the fate of their friends. But there is no time to mourn.
She has never mentioned that her abilities will not work with beings that are out of phase.
Nevertheless, being out of phase and being unreachable for both ship's sensors and telepathic/empathic abilities, may suggest the reason. It is still a guess, though.