1). When you use a select tool it selects all entities on layers within its tolerance. If you have one line on top of the other one (e.g. water main line on top of street center line) then both lines are selected.
It would be desirable that select tool would select only the top layer – the way it works in MapGuide 6.5.
2). Also, if you would turn of layer in the legend and some entities are selected on this layer (e.g. you selected a water main and then you turned off water main layer) then the selection is still visible even the layer is not. It is confusing for users and again in MapGuide 6.5 this functionality works right, contrary to MGE.