If you read the detail on Flightblogger, it details how this is a manufacturing issue and not a design problem.
I disagree. Tolerances are something which happens during manufacturing just like rain will happen during operation. When building from composites, more tolerances will happen. Not properly taking this into account is a design deficiency. There is always a way to design structural details in a way, that tolerances can be compensated. Shimming typically is the least favourable way to deal with it, as it adds weight and is prone to yet another tolerance issue (especially if tapered shims, individually produced to close tolerances are required). Designers with experience in manufacturing and repair will find a way to handle the issue, designers knowing just their computers will have to rely on the manufacturing people to correct for their shortcomings. If things like this happen, the design is as much responsible as the manufacturing.