Though not an expert, I have owned a few V&Cs, and your concerns are justified if they are, in fact, holes.
It is difficult to imagine how applied markers might have been removed and reapplied without guiding the posts into the correct holes. However, if they were, in effect, sheared off, and the posts left flush in the dial, it is possible, I suppose, that they might have been reapplied inaccurately with an adhesive.
Frankly, given the apparent very good condition of the rest of the watch, it is odd that the dial might have required cleaning to begin with.
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