There is a problem with the current 0.12.11 version. by adding shield penetration Walt broke the basic penetration power interaction with shields.
that means that right now any missile with penetration power (like my drill missile, Udrill missile and drone mk2) will harm directly the shield generator and destroy it by hitting the shield.
edit: i have found the issue. it will be fixed next upload with a new weapon that will do exactly like the problem i had, destroy shield generator upon hitting the shield.