I've been encountering this problem since I performed the upgrade as well. I have restarted (typically a couple times a week). I also discovered that toggling the contacts off, and back on would "fix" the issue. Unfortunately, the "fix" doesn't hold on my iPhone 6. It will work for that use, but I have to toggle 2-3 times a day (basically every time I go to make a call and want to use the search function instead of scrolling through 400+ contacts).
I don't want to Show all Contacts because I don't want wee through my Facebook contacts all the time. I don't really know that Showing all contacts is any more permanent a fix than toggling my primary address book off/on.
Do we think there is an update forthcoming to address this?