Silicone rubbers tend to be thicker in viscosity. This means that when you mix by hand there is often a lot of air that gets in the mix causing bubbles in the mold. Although these bubbles rarely appear on the inside face of the mold, they are still in the body of the mold and may weaken the rubber.
Internal bubbles can also cause surface dimples on the cast parts. The exothermic heat from the resin casting process can expand the air in the silicone mold bubbles and cause dimples on the resin part.
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