Blinking yellow means the turret is in transition.
So something went wrong there.

Either it's "natural": the turret is blocked by something and cannot move where you demand it. In which case investigate the problem, fix the leaks, electric components etc...

Or there is a bug and the turret was not correctly initialized at the beginning of the round or somethng like that.
In this case you can reset the shuttles to the shop.

Generally I advise to end the round with the turrets in the default position, the game doesn't manage multiple docking options for shuttles very well.

warning lights are blinking