The phrase is actually a reference to an old puzzle. A web search on "nine dots puzzle" will find it. The puzzle shows an square array of nine dots in three rows of three. You are challenged to put down a pencil and draw four straight lines, without lifting the pencil, that will go through all nine points in the box. The traditional solution involves drawing a sort of arrow shape, with two corners that project outside the boundaries of the box. One reason why the puzzle is hard to solve is that people feel constrained to stay inside the boundaries of the nine-dot box, even though the puzzle does not say you need to do that. "Thinking outside the box" means not to be constrained by requirements that aren't really part of the problem statement.

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