It isn't a bug. It is the result of having only one shield layer and having to make a design decision on what happens when using both types of shields. Combining phased and non-phased shielding has resulted in a non-phased shield layer since at least SE3.
Never paid that much attention to it.... cant remember ever using mixed shield types in any design other then Devnull mod. No reason too. I always tried to reach phased as quick as possible and only put phased on my ships.