I've noticed that in some occassions the shields of scouts don't replenish after a battle.
It happens when the surviving ship completely looses its shields and part of its hull strength.
The hull strength builds up to its maximum value, the shield stays at zero. It happened to my ships as well as the ships of the AI.
I've noticed it while playing with different races.

does that ship have shield type 0? It's a wanted feature that those (as the weakest shields tech-wise) cannot replenish once down. I am myself not much acquainted with that situation since I do not use type 0 shield ships, but does it replenish again, when you hit home and get to a nearby starbase or shipyard to repair the ship?

The ships probably all had shield type 0 now i've come to think of it.
The shield do not replenish even when in own system with shipyard or at a outpost or starbase.

I experienced this problem too, in my initial game I played as the Rotharians. I could get the scout's hull to repair by returning to base, but nothing I could do would get the shields to regenerate.