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I do not think the reason is "because light transmitted through a window is incident on the inside of another window", there is nothing about that would be expected to be a problem. It is quite common in rectangular corner zones.
This is probably coming from two surfaces (named in the message) that intersect and sort of pass through each other (or maybe non-convex surfaces or a surface whose vertices are not all a single plane). As the warning says "Check Surface Geometry" for these types of issues.