I experienced the same bug last night (on a post patch3 new campaign). To clarify, it happens when only part disembarking a stack loaded on a fleet at port. i.e. selecting one of 2 units for transfer from ships to land and clicking on the transfer button.
I haven't tried this when landing troops away from a port.
Disembarking the whole army and re-embarking the desired troops back on the ships is a work around.
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