[Suicide Junkie]

That's almost certainly shield regenerators and partial damage at work...

When you hit the enemy's hull with your APB or shield-skipping PPB, it will kill some components, but there will usually be a little bit left over that can't kill the component it hit (usually a weapon or armor).
This leftover damage gets added to the next hit.

But, if the next hit is blocked by the shields, then that leftover "hull" damage got moved into the shields.

On an APB hit that should be doing 60 damage, you might see:
-15 / 75 .
Total = 60.

The Organic armor is a different effect...
As the armor regenerates, the component pictures will change from the bLast hole thing back to organic armor pics as they get repaired. The hitpoints count dosen't get updated until the next weapon hit, though.
Hence, if you bLast them down to 100 hitpoints, and then they regenerate 100 back in organic armor, and THEN you shoot them for 60 damage...
The game says: they now have 140, they had 100 after the Last hit, so that makes "-40" hull damage.