Think it was intentional. If I recall correctly same thing occurred in beta as well. If you happen to move into a subs hex the ship attacks the sub. Not sure if BB will do this also or not.
All heavy cruisers have a submarine attack but lack the sonar feature of the DDs. There is also a generic light cruiser for all nations that can attack subs and has even sonar. There haven't been any changes there by the patch.
You can detect submerged subs with all ship classes when you move right into the hostile sub's hex. You will hear that pretty alarm sound then. You won't detect the sub when your ship moves through the hostile sub's hex though.
It's not that plausible of course, but there is no other way in the game to prevent two ships occupying the same hex, so either you deny the target hex for unknown reason or make the obvious invisible occupant detected.