To ensure your running workouts from other app, such as Nike Run Club, are synced with Habitify, make sure that the data has the attribute "Workout type" set as Running. You can verify this by checking the details of the data log saved by in your Health app.
Additionally, be aware that using scalar units for habit goals will not work with health tracking. For synchronization to work, the unit of the habit goal should match the unit of measurement you want to track in Health.