Yeah, now there is the potential for one buggy app creating bad data to "infect" all your other apps via HealthKit. Like if it doubles up your runs, now your activity calories are wrong in your diet tracker. Yay.
One of the protections there is that if you delete an app from your phone, you've got the option to also delete all of it's data from HealthKit. Still agree it's a pain though when it does happen.