Frankie phoned Fallon from the car phone to tell her she'd been kidnapped. Fallon then told Jeff & Jason. So those three knew.
I’m tantalized by the thought that if the plot for Season 3/4 called for Fallon to be hallucinating that spaceship, then could she have been hallucinating other events? Was she having some sort of mental blow-out that rather perversely enabled her to pick up on stuff psychically? Like Frankie’s distress. So strong that Fallon really believed that Frankie phoned her and spoke to her about being kidnapped -- though Frankie may not have actually gotten through to her, or perhaps never even made the call. (If viewers saw the spaceship that Fallon never got on, then it’s possible viewers saw Fallon receiving a phone call that never happened or which didn’t actually play out as they thought.) It could have turned out that Fallon, in her mental condition had believed Frankie physically phoned her about being kidnapped by Philip even though Frankie hadn't. End result: J&J went chasing that car.... Basically, anything that's connected to Fallon from the time she went off the handle when Henderson told her about the phone call is suspect.
TC always had a twinning theme… Similarly, Zack told someone something about Philip and that got conveyed to Jason who then told Jeff – except that, observant viewers knew that there was clearly a question mark over whether the incriminating evidence in hand was what it seemed…. I fancy the plot for Season 3 was going down the route that there would be next to nothing by way of good evidence to tie Philip to upsetting events. There would just be this thick cloud of suspicion around him.