This has happened to me multiple times, and I've noticed this bug with both air and naval transports. It happens under these circumstances: when I'm carrying large numbers of troops on several transports, but not all the tranport capacity is filled to the limit. If I'm splitting my stack of transports and troops into several smaller stacks to go different directions, it sometimes leaves behind some of my troops in the water without a transport, while the main stacks moved on... It's rather annoying. Do ya'll know what game mechanic(s) cause this?
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"For out of the ground we were taken
For the dust we are,
And to the dust we shall return"