A) It was traded and you weren't paying attention to your 3DS. As in, just pressing the a button to get online and absentmindedly looking away while the trade animation plays.
B) There was a glitch and it didn't recognize your pokemon. Log off and log back on.
C) There was a glitch and your pokemon is gone. It happens, but that's why nobody puts anything important on the GTS. --- Currently playing: Pokemon Y (Name: Ensei), Xenoblade Chronicles, 3DS FC: 2277-7562-5299 FS: Ghost @ Drfiblim, Lampent, Pumpkaboo Steel is superior.