A unit created by the captured vehicle factory is invisible for enemy forces.

[SergeYunev]

And again about seenByHouses.
When an enemy unit enters a structure and captures it the structure does not inherit unit's seenByHouses. It means that a unit created on such factory gets the factory's seenByHouses and becomes invisible for enemies.
I think in this case when a unit captures a structure the unit is more meaningful that is why the structure must inherit some unit's properties.
It means in the block (Unit_EnterStructure)

if (s->o.hitpoints < si->o.hitpoints / 4) {

the structure should inherit unit's seenByHouses value being previously reserved because of

Unit_Hide(unit);

which clears the seenByHouses value.

[SergeYunev]

I think the problem is actual not on every map, because it depends on initial value of the structure's seenByHouses. I observed it on the last level when playing for the atreides and when capturing the harconnen's vehicle factory.

[miniupnp]

@SergeYunev could you upload a savegame so we could reproduce easily