This isn't so much a bug as exactly how leaky shield systems are meant to work. Of course, STM shields aren't the typical brand of leaky shields, but they still have the shields from damage feature. The shields are added after the damage is done to the hull. Unless you have very high hit point per component armor (such as 150 points), some components will be damaged with each shot that hits the hull. Then, the next shot will have to go through the shields.
Typically, high damage per shot weapons are the most useful in a leaky shield system, especially when larger ships come into the fray.
Any weapon that skips armor will prevent the shields from damage ability from triggering. This includes stock game null space projectors and shard cannons.
More information on leaky shields can be found in
SEIV Modding 101.