The issue is not necessarily quality issues in production.
Whatever part you manufacture, you will have tolerances. It is unavoidable. Especially if you assemble a complex machine from thousands of parts you need to design for tolerances, you need to have provisions in your design to account for them. For example shims.
You need to design for that, you need clear (and workable!) shimming procedures for production. You need to plan for the time it needs to perform this.
The new generation of CAD designers which have never seen production tend to believe that if they specify the dimensions in their computer model to the third digit, it will fit. It won´t !
Composites generally means higher maunfacturing tolerances than metal, and of course in other locations. The wound fusealge barrels of the 787 do not allow any diameter adjustemt, you need to plan for it on the mating parts. If you need to join two non-adjustable parts, you have messed up the design. If you do not realize that from the very beginning and design for it, you will face the issues Boeing does just now. again...
There are reasons, why the A350 fuselage is made from large scale panels, not from seamlessly wound barrels.