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Some polygons may be created within a larger polygon using the auto-complete polygon tool. Using the Select by Location tool to select features that 'are completely within' the features of a given layer does not select the newly created polygons.
The newly created polygons share boundaries with the features of the specified layer.
In this case, the correct option for the Select by Location tool is 'are contained by'. Using this option will allow the newly created polygons to be selected as expected.