Insider's View
The clock "vendor" Intel uses has a solid history of reliability. The problem, in my opinion, is most probably Intel's implementation of the Atom's on-chip clock domains. Probably specs are loosening after the chip is heated over 18 months.
I have a hard time believing that Intel didn't catch this during QC testing, as some tests subject the MCU to intense heat over a short period of time. It would have caught this. I suspect middle-level managers inside Intel knew about this and didn't tell upper-level managers.