You have to remember the boss’s name

Axel, having become Roxas’s teacher, makes him say their boss Xemnas’s name. In Kingdom Hearts 2 when Axel tests Roxas on whether or not his memory has returned, he says the same line.

What's our boss' name?

She woke him up

Just before Roxas wakes up on day 50 he hears a girl’s voice. The voice is Kairi’s, saying the same thing she said to wake Sora up at the beginning of the first game. Before and after this scene we see Xion taking care of Roxas. Does this show some connection that Xion has with Kairi?

You lazy bum, I thought I’d find you snoozing...

A promise to go to the beach

On day 224 Axel, Roxas and Xon make a plan to go to the beach, and a Secret Report on the same day talks about “watermelon and pretzels [jp vers: yakisoba].” It makes you think of what Hayner said in Kingdom Hearts 2.

On our next day off, want to go to the beach?

Pretzels [yakisoba] of course! What else is there?

Giving up already?

On day 297 at Castle Oblivion Roxas loses conciousness but is woken up by someone saying “Giving up already? I thought you were stronger than that.” This is one of Riku’s lines from Kingdom Hearts. On day 358, Riku says the same thing to Roxas to try and get him to show his true self.

Giving up already? I thought you were stronger than that.

The sadness of losing the keyblade.

On day 321 Roxas has a dream from Kingdom Hearts when Sora, the Keyblade Hero, loses his keyblade to Riku, and cries. After this Xion starts replacing him as a keyblade user.