The article is light on details, only stating: "...a worker at a Boeing supplier flagged that two holes in the plane’s fuselage may not exactly meet specifications."
This statement is missing the information needed to grasp the seriousness of the issue. For example, if 100% of holes inspected (very unlikely), then 2 nonconforming holes out of hundreds of thousands of rivet holes on large craft might be acceptable and possibly even within acceptable quality limits; however, if the inspection plan calls for random sampling of two holes anywhere on the fuselage, and both of them happen to be nonconforming... not good.
Non-conforming rivet holes may have many underlying causes. Even if they are missed during panel fabrication, a nonconforming hole is likely to cause a rivet installation failure, which are likely to be caught by downstream quality control processes.
If by "closely", you mean "check every single rivet hole on a large commercial aircraft", you are going to quickly discover just how difficult this problem is. The tolerances are extremely tight, the holes are very small, and you are often actually dealing with multiple holes and sealant layers (a rivet holds multiple sheets together).
I would be stunned if any large aircraft on the planet has 100% perfect rivet preparation.