There are a lot of lies in the book Ender's Game. Many characters lie to Ender for a variety of reasons, but the character that probably lies the most is Colonel Graff.
Colonel Graff does genuinely love Ender. He wants to protect Ender from harm (physical and emotional) as much as possible. That's probably why he lies to Ender about all kinds of things. More often than not, Colonel Graff's lies to Ender are not outright, blatant lies. The lies that Graff gives are done by him not giving Ender all of the information. Graff lies about the boy that Ender "beat up" (killed). Yes, Ender did beat up the kid, but Graff hides the fact that Ender killed him. Graff also lies about what all of the computer simulations are. Mazer Rackham is complicit in this lie too. Ender thinks it is just a computer game, but he is really controlling the human fleet through their battle with the bugs.
I would say that their main motivation for lying is to protect Ender. They know that he is in a fragile emotional state, and they worry that the truth will make him incapable of doing the job that he needs to do. That reason also flirts with selfishness. If Ender can't do his job, then everybody dies. So by lying to Ender, characters like Graff are protecting Ender and themselves.