It appears that even if you have the Auto Repair and Autorefill Ammo boxes checked in the EQUIP screen, it won’t stay when you have logged out.
When you log in, the boxes will still be checked but it won’t refill ammo or repair? You have to uncheck and recheck the boxes to make it work again.
At the moment there is a bug that causes that after every log out your rockets are unequipped.
But the auto repair should work without any problems.
Oh I see, noticed that too 
Thought it was wierd because shop options are saved when you log out for some reason.
Thanks for the report and I hope this bug will be fixed in one of the next patches.
At the moment there is a bug that causes that after every log out your rockets are unequipped.
But the auto repair should work without any problems.
as long that ship that come back with you after battle, the ship you left in fight for another fight using other ship still bugged and need to be repaired manually
To fix this have auto on all ships. Make sure you have enough ammo in stock to cover all ships should work fine. However it is buggy sometimes still have to restock manual
i have auto repair and refill on all ship, just the case i mention above still occur
/fixed closed moved.