All 3 of those features are visible; it's just that the merged feature is drawn last and hides the two smaller features that are in the same location. There's no real way to tell which feature is "on top" but from my own observation it always appears to be the feature with the higher ObjectId. My guess is that ArcMap renders the features in the order of their ObjectIds but I'm not certain that is always the case. If you need to be able to identify the merged features from the original features within a feature layer then I would suggest adding a field to the layer's attribute table that holds this information. You can then add an attribute query to your spatial filter in order to get the results you are looking for.
