Everybody else within Homura's labyrinth had their memories altered, except for Sayaka and Bebe. Why was this?
It was because Sayaka and Nagisa (aka Bebe) came with Madoka and were entrusted with Madoka's powers and memories.
When Madoka went into the barrier she knew it was a trap set by The Incubators as such she entrusted her powers and her memories to Sayaka and Nagisa and fool The Incubators.
It's revealed that Madoka, Sayaka, and Nagisa didn't have their memories altered by Homura's barrier. Instead Madoka entrusted her memories and powers to Sayaka and Nagisa in order to fool Kyubey. Sayaka and Nagisa simply played along with the barrier while waiting for the right time to reawaken Madoka. Sayaka admits that while it's caused them quite a bit of trouble, Homura has been trying hard and deserves her reward.
It is hinted beforehand that Sayaka has extra knowledge as after Homura and Mami fought Mami remembers that their enemies were the Wraiths not the Nightmares however Sayaka remembers the Witches and that Bebe/Nagisa is taking the form of the "Desserts/Sweets Witch"1 (understanding why Homura suspected her to begin with). she shouldn't know what Witches are however because in Madoka's Universe they don't exist.
Also because they played along there was no reason for Homura's labyrinth to try and alter their memories, but i also like to suspect the divine nature of Madoka's powers that they had been given provided some protection since the barrier was one way and only invited people in. Madoka was invited and maybe Sayaka but Homura would have no knowledge of Nagisa and even if she went in as Bebe (thus looking like Charlotte's first form) she was never invited in and i would think that the barrier would try something at first but when Nagisa played along it then just decided to factor her in
1: Depending on what version you see Sayaka will call Charlotte the Sweets Witch or the Desert Witch