My supply wagon surrendered to me (and missing units, troops just ran for their life)

[Best Waifu]

So that happened.
 

[LAVA]

You get 7 units in that battle and you appear to have 7. So, I'm not sure what you mean by "missing units."

You have also pushed very aggressively and successfully against the Confederate forces as the time is 5:51 and it is dark. The confederates have, I believe, 4 infantry brigades, 2 skirmisher brigades and 1 artillery unit in that scenario.

If you push directly on the objective and take it, the AI has a tendency to send it's troops to the right side of the map. The only way to detect them at this time is to occupy the observation point to the right of the objective.

Hard to say what happened here, but since you don't have a unit on the observation point to see the map, my guess would be that a Confederate skirmisher unit sneaked in and captured your supply wagon.