If multiple sources contribute the same data type, the data source at the top will take priority over the other sources. Any new apps or devices that you add go to the top of the list automatically, above your iPhone or iPod touch.
An alternative option is to turn off the Fitness Tracking feature of your iPhone, this prevents the Health app from counting steps from the movement of your phone effectively limiting the Health app to using your Apple Watch data only. The Fitness Tracking feature is found in your iPhone's settings under Privacy & Security ->Motion & Fitness
If the information above does not help to correct your data within Apple Health this is an issue you would have to address with the Apple support team as it would be an issue with how the Health app is interpreting the data it receives.