Pet Peeve: When people who either watch the show or read the books call Daenerys "Khaleesi" with no other descriptors. Khaleesi is a title, not a name.
For example, imagine holding this conversation about your friends:
"So I got a call from Postal Worker the other day, he asked if I wanted to go to a party he was having. I told him I'd get hold of Blackjack Dealer and Hotel Clerk and get back to him. Really, I'm not sure I want to go, especially if he brings History Teacher there. History Teacher is a drag at parties."
Would you do this? I'd expect you would call them by their names, not their positions. Now it's different for people who are actually in the GOT world, they're calling her Khaleesi in much the same way as we might call Obama "Mr.President" or the Queen of England "Your Majesty" as it's an honorific to her. The difference is, they're talking TO her, not ABOUT her. When they are talking about her, they call her Daenerys, like any normal person would.