Speaking as an engineer, you're supposed to design for the worst-case tolerance stack to be viable...
If 0.01% is out of spec then you need tighter tolerance specs on your individual components or otherwise your design does not mathematically make sense.
This sounds like a design and process control issue as much as anything.
It is a process control issue, the problem is that controlling the process when you have 100 of sub contractors manufacturing parts which are pre-assembled in 10 different locations and then sent for final assembly isn't that easy. And even if you add tighter tolerances to the spec you can still end up with things not working properly.
Not to mention that increased tolerances means higher costs and there's a point where you can't adhere to them physically and as far as real world manufacturing goes the tighter your tolerances are the tighter the control and QA needs to be which results only in diminishing returns.
When you end up manufacturing things tolerances can be skewed by a 100 different reasons from a slightly different zero and certification process to different CAD/CNC software which rounds up thing slightly differently.
The ISS development actually learned quite a few things with that and they've both adjusted their process segmented the manufacturing by entire modules rather than individual parts then the only thing you need to really worry about are the tolerances for the actual dock which have quite a bit of wiggle room.
If you had to make the frame for the cupola in Italy, the outer housing in France the Windows in Germany, the Shutters in the Netherlands and assemble them in the UK you would ended up with similar problems.
Saying there's nothing wrong with X you just need a better process can be said for pretty much everything but that argument rarely holds water when you deal with real world applications, there's a reason why there are entire engineering disciplines for manufacturing and process control.
So no as an Engineer you need to design tolerances not for the worse case scenario but for the actual manufacturing process you are using and the controls you can enact on that process.
When that process is then spread out across as many parties as possible it's no longer the process you've started with and quite likely isn't neither and ideal process nor one you could ever really optimize.
There's a good reason why some of the worlds most advanced engineering parts are still quite often hand fitted at the end, and that's when you work with a single manufacturing process in a single factory.
When you spread that out you end up with parts that sometimes can't even be hand fitted anymore.
If 0.01% is out of spec then you need tighter tolerance specs on your individual components or otherwise your design does not mathematically make sense.
This sounds like a design and process control issue as much as anything.