Besides it being a bug (and of course; if you passed the time limit), the only reason the NPC would say this to you is if you made use of one of the Keebacorp transportation systems (being the ferry, train or aerial tramway). If you didn't use any of them during your trial and you're adamant about finishing it in 25 minutes, I would suggest you'd try to record your next "run" and post it in the Bug Catcher section on the Playerdex, cause sometimes bugs do occur. Even if it ended up that there wasn't a bug; it would still result into answers in the form of feedback to correct possible mistakes.
I hope your issue will be resolved soon.
P.S. You have to heal at a Pokemon Center nowadays to set it as a teleportation beacon.