Bug has only recently started happening, and I'm not sure it's consistent. It's happened on at least two occasions, the first time I thought I had made a mistake myself. OK. Ship is out on the high seas, meanwhile I'm raiding with my crew in multiplayer. After the battle I return to the layout with my survivors and retrieve the additional troops by clicking on the ship that's returned from travels. Together they fill the camps. I check the exploration map and get the result of the battle, a number of troops died. At this point, the troops are removed from my ship. That means that instead of having a full ship for exploration I now have half, and have to go back and re-cook. It doesn't make sense to me, and I really doubt that this behaviour happened previously.
Browdside: i have seen this behaviour also in the last few weeks. Ship returns with 20 or so Pirates aver a map voyage. Soms clicking / action in the menu's and .. POEF! 6 left...? Feels like the unit count forgot the löss of the last sea battle and corrected this.
This has been reported in many other threads already and is a known bug. Make sure you collect all your rewards from monsters before rehiring so that the troops are properly removed from your tavern prior to your next voyage.