That's a bloody awful photo of the layered area. Your phone has focussed on the ground behind giving us just a blurry shot of the branch which gives us very little to go on.
Some junipers have red bark under the outer layer of grey bark. If that's what you have it means you did not go deep enough when you cut. Fresh wood is white and shiny so need to cut right down to that smooth, shiny white wood to layer.
In many junipers I have noticed the exposed wood changes from white to various red colours when exposed to air. My guess is this is oxidisation of some of the chemicals in the sap or wood - similar to how a banana or apple turns brown when cut. That will not affect the layering process so is neither good nor bad.
Photo does not show any roots so can't make comment on roots below? the layer other than to say that some junipers layer very easily so some extra roots below the cut would not be unusual.
It would help a lot if you mentioned how long ago you made this layer.
It would also help if you say where you are because seasons are different all round the world. What's good in one place may not be so good in another place. Best is to update your profile to include a city or location. That info comes up with each post and saves you having to type it over and over.
