I think the illustration below gives some insight into what I believe the problem is that Boeing uncovered and is dealing with. The cartoon that is inside the rectangular box depicts what happens when the shim between the stiffener and the composite shell doesn't close the gap and the fastener is tightened. Initially, there would be no noticeable problem, but over time, the stresses set up by this condition and the fact it is at a hole (a natural stress riser) in the composite material eventually could lead to delamination at the hole location. I am sure the detected flaw/flaws can be repaired.
The particular composite Boeing is using in the 787 fuselage application is very strong, more comparable to high strength steel than to aluminum. The composite behavior is different from aluminum. Impacting aluminum causes a dent, taken to extreme, it causes a dent and fracture. Impacting this particular composite result in no dent up until the point the tensile strength of the composite is exceeded. Then it will begin to delaminate meaning separation of the built up layers.
I hope this helps the understanding.