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Overlapping isn't necessarily a problem, it would only be a problem if the page shifted a great deal (skewed or warped). The way the program detects bubbles is it will create a silhouette of each enclosed blob, then it will look for the mid points of each blob and see if it matches the number of columns/rows that are equidistant. It starts the match procedure from the middle row to the edges, a row of mid points by a row of mid points. Eg. Middle row first, middle row - 1 on the y axis next, middle row + 1 on the y axis after that, middle row - 2 on the y axis after that middle row + 2 on the y axis after that and so on.
The short answer is that if the correct row is closest to the center of the fragment, it will work fine.