I get step data from both my watch and my phone, and when the iOS app adds datapoints it seems to sum the two rather than de-duplicating them. In Health I see about what I would expect as far as totals:
Here’s the data from my watch & phone:
Note that the Beeminder datapoint is the sum of the two for today (October 10), though it should be 5,359:
It’s fairly common to have multiple apps/devices contributing data to health, so I’d be surprised if there isn’t an API in HealthKit to get the de-duplicated data.