There is a problem with Pulsewave attacks in shooter mode, when shooting for example the giant or small turrets, or the generators in Cure Ground.
It's a problem with other non-humanoid hitboxes as well.
For example the generators in Khitomer Ground, or destructable doors in the story missions, etc.
You seam to have to aim for a very specific part of the model or pulsewave shots will do no damage, even if the crosshair has turned red.
I could only really tell where to shoot by checking the object with another weapon, and seeing where the beam effect goes to.