He probably should have waited to ask that question, or at least just asked Galen, if the look in Jyn's eyes is anything to go by. It's nothing overt, not like she suddenly knows everything, but it's probably too much questioning of Krennic on his part.

Instead, he focuses on the reluctance in the word guest and the clear annoyance she has with his presence, however much she's attempting to pretend otherwise. He says a quick thank you to the server first, but then to Jyn, "And I appreciate you and your father letting me be a guest. I know I've had a lot of questions, but the sooner I get a sense of routine here, hopefully the less I will feel like a guest who needs this much attention. I don't want either of your own routines to be altered too much by my being here."

That would definitely counterproductive to getting on Jyn's good side. Even if he's sharing her room, which is probably going to be the biggest hurdle and change in her life.