Please make sure that the iPad bracket is firmly flush on both sides.
Please also make sure that you aren’t using the Wide Vision Lens.
Could you please post a picture of the issue you are seeing on the Scanner App?
What iPad are you using with both your Unity App and the Scanner App? Could you also post a picture of your iPad with the Structure Sensor attached?
Could you, finally, send us a screenshot of the alignment phase of the Calibrator app? This is the phase where you align the color image to the depth image after the short tutorial.