I felt that it would be a bit too cruel to reset progress with how difficult the game can be, so yes that is intentional. During the DAD fight you are supposed to pet by left-clicking on a space not currently occupied by DAD, but looking back it seems that I need to communicate that better since it goes against all of the previous mechanics of the game (shooting forward). The locking of the player's ability to shoot is definitely unintentional. I'll try to patch the fix in sometime soon.
Really appreciate the criticism, it helps a lot. Glad you still enjoyed the game!