The video below best illustrates the problem. I first alt-click on a MeshPart to select it. I then shift-click in the explorer to select all children of the Model. This does not work as expected and skips over a few instances. In some other cases it even selects a bunch of other objects in my game.
If you select the object through the explorer and then shift-click on the instance inside the explorer, it will work as expected. This problem may potentially be related to this other bug report that was posted recently.
Although this is a very minor bug, it would speed up my workflow a lot if this is fixed. Currently if I want to recolor models in my game for a winter update I have to re-select a lot of objects before recoloring them due to this bug. 