Well, as of the latest update (version 1.1.0), this small oversight in the second secret area of Bianco Hills has been fixed up.
We had a look ourselves and can confirm the cubes are no longer visible in this section of the game:
When these debug cubes were originally discovered, The Cutting Room floor shared the following information:
"Presumably due to imperfect graphics emulation, these cubes were visible in the Super Mario 3D All-Stars release of the game."
Are you glad to hear these debug cubes have now been made invisible again? Or did they make it easier for you to navigate this secret stage? Leave a comment down below.