I like seeing my upcoming appointments in the notification view, but I have several subscribed calendars that I generally keep turned off, but keep around so I can reference them when necessary. They're showing up in the notifications and I don't want them to.
To the best of my knowledge you can't fix this. Hopefully Apple will modify this in an update at some point, but who knows. For now, the notification center is useless to anyone with a complicated calendar system.