Yes! This is a huge problem for me, it affects a ton of apps (but not all). The ones I've noticed are: Apple Watch, Activity, Calculator, Wallet.
It seems to only happen when you restore from a backup from an older device (i.e., my iPhone 5s in my case). When you set up as a new device, it works as you would expect.
I called AppleCare and they basically told me that my only option is to scrap all my data, set up as new device, and load whatever I can back from iCloud and cloud services.
Really, really disappointing.. hope we can bring some attention to this. Some folks over on this Reddit thread are having exactly the same issue:
https://www.reddit.com/r/applehelp/comments/3mebxx/is_anyone_else_having_a_problem_is_wallet_being/