If I start to recruit pirates, then click on a completed voyage to bring the ship back, some of the recruiting orders are being canceled. (I haven't kept a close enough eye to see if I am being refunded the hire cost, but I most likely am not?) This happens even if I send the ship back out on a voyage with its original crew before any new pirates are recruited. So say I start recruiting the max of 20 pirates. Then while they are being recruited I bring back a crew of 3 and immediately send it on a new voyage. Only 17 pirates will be recruited and if I look at the orders, 3 of them have disappeared.
You won't get a refund of pirates. They're looking into a queuing system to remedy this. Not sure if it's arriving with the next update, but rest assured it's being addressed.