I dont think there is really a bug - only things that might seem as if moves are lost. In fact there are no moves lost you dont want to be lost.
Just a quick introduction into the game mechanics as i understand them:
You set the destination of a ship by clicking on a position. If this position is not reachable with the amount of left moves, the ship will go into auto-pilot state and continue following this path. The autopilot moves are executed upon clicking the turn-button right at the end of one round before the beginning of the new, so you can manually correct the route before turning. This is point 1, which may make it seem the ship lost moves. It moves at the end of the round, not at the beginning.
That means - you move a ship in the beginning of a round to a point beyond its reach. Supposed it has 1 movements, it has 0 when stopping. You click turn, it gets 1 move, next round begins. It doesnt move - if you do not intefere, it moves by itself at the end of the round after you click. Now you have the satisfying feeling, that every click causes a move. BUT - like me, you are one impatient chump, so you decide to click on the target again next round. The ship does its move, now at the beginning of the round. You do your other stuff and click turn. You forgot, that the ship already has done its move, you look at it and what does it do? Of course, it does nothing, it stays where it ist (1 move forward) and the next round begins, it has one move, but not moved. When you click, it moves but again the turnbutton does not move the ship. This gets quite irritating with lots of ships moving on the map, because you may think moves get lost when you do not manually control the ship. If you would not have moved it before clicking turn, it would have moved on its own before the next round begins - no move lost.
As you may understand now - its just an illusion, that is a result of the game logic that manual moves are executed before clicking turn, automatic moves after clicking the turn-button which may confuse your perception of the round it is executed in.
Another thing where moves really can get lost is the "skip moves left over from autopilot" option. This means, the auto-pilot ships go to its destination. (Auo-piloted ships always get to their location with the minimum moves needed) When arrived, you are noticed by the screen jumping to its location and the "skip" button appearing. Clicking skip means, you just ignore, that this ship has no more destination and stands around like a bum, just going to the next inactive ship, until no more are left and again the turn button appears instead of a skip button. Enabling the above option has the same effect as clicking skip every time.