Happened to me twice today:
Someone I am spectating is playing a map I definitely have, but the game says I don't have the beatmap the host is playing. First time was just with a friend and he ed the map via my /np command, so it definitely was the same map. We also doublechecked if one of us needed to update their map but that was not the case. It only happened with that one beatmap, everything else I could spectate just fine.
The second time was spectating the World Cup. Really bugs me that I didn't get to see that one xD Again, I definitely had the beatmaps and they were updated to their latest versions.

Is this a known issue?

I can add one more situation. If you spectate someone playing map you have, and just before he/she starts playing you press F2 for random map, you'll end up spectating wrong map but with the real clicks of player.

Which map was it?

http://osu-ppy-sh.tvgratuite.org/b/45461&m=0
http://osu-ppy-sh.tvgratuite.org/b/46955&m=0
http://osu-ppy-sh.tvgratuite.org/b/48926&m=0