The spotlight window occasionally resets almost completely off the bottom of my screen. It gave me a fright the first time it happened, as it didn't appear that spotlight was working at all, even thought the process appeared to be running in the activity monitor. I (finally) noticed just a tiny edge at the top of the spotlight window was visible. I moved it a couple of times to my preferred (upper right) part of the screen. It's been a few days now, and no movement for me.
Try moving your spotlight window each time you boot, or restart, or wake up your Mac. Even if it has not moved since the last time, move it out of position, then back. Maybe it will remember after a few times - or just something that should be fixed by the final release of ElCap.
So, yes, a bug. You're not on the final version of El Cap yet, so report it to the "home ship"