If you are playing simultaneous movement, you can order the ship to move into the sector it is currently in. It will do nothing, but it will not appear in the cycle, as it has an order. There is nothing you can do in sequential (turn based) movement, other than sentry the ships, which remains next turn.
Well, you could move them around and back to their current location to clear their movement, but this wastes supplies if they do not end on a resupply depot...