Quote Originally Posted by phoule
This appears to be a bug. It also happens to regular units, but it's less noticed as you see less full stacks of units needing retraining simultaneously, because most people don't auto-resolve if they can avoid it meaning more units sustain no casualties. What causes it appears to be having a full stack of units (no room to add anymore unit cards), apparently the game refuses to add units to an already full stack regardless if it's only to just top up existing units for retraining purposes or a fully trained stack that has no room left.

The work around is to leave one space open in your stack so it can retrain the appropriate units, the only thing that really sucks about it is when you're in hostile territory and have to place a unit outside your city in order to perform the retraining as your whole underpowered army will be pulled into a fight if that lone unit is attacked unless you place it far enough away from your city.
Tried taking a ship out and they retrained no problem. Thanks for your help