Many Bones Elite and Super Elites have small holes visible near the hub of the wheel.  This is a known element of the process by which these high quality wheels are made and do not affect the performance of the wheel.

The bubbles are caused by the viscosity of the material and the creation of some bubbles as the material enters the mold.  In materials with lower viscosities the bubbles rise and pop before the material solidifies, but with this super high performance material, the molecular weight is higher and this causes the viscosity during processing to be higher too.  Bones could use a lower viscosity material, but then they would not be Elites....