I am sure there are analogous problems in the digital simulation domain. Without thorough oversight and testing through multiple power cycles, it's difficult to predict how well the circuit will function, and how incorporating feedback into the program will affect its direction, if not careful, causing the aforementioned strange problems.
Although the article mentions corrections to the designs, what may be truly needed is more constraints. The better we define these constraints, the more likely correctness will emerge on its own.
This problem may have a relatively simple fix: have two FPGAs – from different manufacturing lots, maybe even different models or brands – each in a different physical location, maybe even on different continents. If the AI or evolutionary algorithm has to evolve something that works on both FPGAs, it will naturally avoid purely local stuff which works on one and not the other, and produce a much more general solution.
The problems just have to be uncorrelated.
I can see it already: cloud provider offers orbital FPGAs for testing your AI hardware designs
For a system you completely don't understand, especially when the prior work on such systems suggests a propensity for extremely hairy bugs, spot-checking the edge cases doesn't suffice.
And, IMO, bugs are usually much worse the lower down in the stack they appear. A bug in the UI layer of some webapp has an impact and time to fix in proportion to that bug and only that bug. Issues in your database driver are insidious, resulting in an unstable system that's hard to understand and potentially resulting in countless hours fixing or working around that bug (if you ever find it). Bugs in the raw silicon that, e.g., only affect 1 pair of 32-bit inputs (in, say, addition) are even worse. They'll be hit in the real world eventually, and they're not going to be easy to handle, but it's simultaneously not usually practical to sweep a 64-bit input space (certainly not for every chip, if the bug is from analog mistakes in the chip's EM properties).
(forgive me, my fellow HNers...)