I do get the reasoning behind forcing a split off army/unit into another square. Essentially, for game balance purposes, you only want multiple stacks in the same square if you are exceeding the stacking limit of any one stack. Otherwise, you could end up with, say if your kingom/empire had a 7 uinit stack limit, 7 single unit stacks, that an attacking player would have to kill in turn, which would take seven turns under the current design, assuming more single unit stacks weren't added during those 7 turns.
That being said, it is nice if we could choose where the second stack is moving to when splitting up a stack. Usually, I select/shift select the ovals of which heroes/units I want in the new stack/take out of the existing stack and then click on the square I want those to move to, and they leave the other units behind, so I haven't experienced this bug you've mentioned. I have seen some weirdness with stack merging/splitting however, especially when cities are involved.
Haven't tried stack manipulation under 0.87 yet, so something might have changed since 0.85 that I don't know about.
