What could be the reason for chip capacitor failure due to silicone potting?
Well, any potting material will put mechanical stress on the board and the components. Any glue or compound, when drying or becoming hard due to its chemical reaction, will do so with the side-effect of changing its volume, even if it happens only ever so slightly. It may well be that one of your MLCCs failed because the compound subjected it to shear stress, maybe worsened by heat.

Also, any chemicals (read: dirt) on the board will remain just there under the potting compound, being trapped forever, and even a bit of moisture might make corrosion effects worse - compared to a board with no potting or coating. This, however, is a long-term effect not likely to be the cause of the particular failure mode you observed on your board.

Try using potting as a last resort.