I have experienced weapons acting funny in really simple missions (not the ones that push your hardware).
The first strange things is when I was testing the rebalanced shivan weapons. I gave them quite a bigger punch - the SF Aeshma has two Shivan Mega Lasers that do 82 damage each.
The thing is when they hit my heavy fighter, that is fully shielded, I loose about 20-25% of my hull, sometimes more!
And the bigger the damage of the weapon that shoots me, the more damage goes trough?!?!?
(In this mission, it was just my fighter, 5 friendly sentry guns and 6 enemy fighters)
The second wierd thing happened when I was texting a quick mission - 2 destroyers duke it out, each with a fighter wing as support. I flew my Lightbringer bomber (with a beam cannon).
Now since I rebalanced my ships destroyers have 180000-200000 Hp and a single hit from that bomber beam can do 3-4% damage. I destroy the enemy destroyer easily and then when I out of fun attacked mine I noticed something strange. The beam doesn't any damage to it! (ship was under 40% HP).
Now I'm stil ltesting things, maby I forgot some flag or something on the beam cannon, but I just though I mention it anyway...