Went to do some NPC farming and found a possible bug when repairing fleets afterwards.
When a battle is won resulting in a number of damaged ships in my fleet, correct me but previously, I only paid for the last ship to be repaired that fought in the lineup
Now, every ship that fought in the battle requires repair causing the repair bill to far exceed any plunder win.
This is especially true when fighting high level, multi-ship NPC fleets where significant damage has occurred to numerous ships in the winning fleet.

I am sure previously, only the last ship in fleet to win the battle was charged for repair ?

That is what I remember too, Stan.

I think that changed quite sometime ago! It used to be the last ship only but then when you attack and one ship get defeated, the next ship takes a turn and so forth. That's why more repairs can happen.
Most similar results found:
1.4.50 (2015-04-21 00:06:06)

Added repair all ships in fleet link, at battle result page.

I did few attacks on fights which I won easily only ship which was in fight got repaird but I did also fight aggainst pirate hunter (without of cards) after I lost that fight I had to repair all my ships.

Ship damages work differently when fighting against NPC than when you fight against a player.

Here is how it works:

Player A has a Sloop and a Cutter at tail.
Player B has a Sloop of War.

Player A attacks Player B and the Sloop of War beats both ships of player A.
Then the damages will be as following:
Sloop of War gets 24% damage.

If Player B was a NPC fleet, then the damages would be as following:
Sloop 99% damage
Cutter 99% damage
Sloop of War 24% damage.

There are reasons as why this works differently ofc.

I have updated the help file for patrols to include this different rule as it was missing till now:
http://s2.piratesglory.com/?page=help&action=patrol