Felix dismissed Ben after assuring him he'd find Kyle, then returned to the Kings Hotel where his presence surprised the staff, and the manager was quickly called down to attend to him himself.
He was yet to visit the Sage Council to clear the air on his disappearance—and didn't plan on doing that anytime soon. Felix had breached their secret lab looking for one of their subjects, and attacked the Titan Capital right after. The arson might also be pinned on him by Titan. So in other words, they knew Felix was onto something, and walking into the Sage HQ at this moment would be walking into a live trap.
Felix at that moment wanted nothing more than to get back to his room and review his gains from the past few days, and so he dismissed the manager and was finally alone. But before he immersed himself with his system, he had a few people to call first. Namely: John, and Elizabeth.
