I don't know how to modify DGen, but in the case of a specific mission if you edit the mission file to a set formation instead of default it has solved the problem in my experience. I think TD needs to take a look at the default formation settings in general.
For example, the Finnish B-239 N1 mission has this bug. Some of the SB bombers collide with the lead flight while trying to form up on it. This results in the player being given the “Mission Complete” message before even sighting the enemy. But if the SB formations are set to Echelon Right formation instead of Default (which looks like Echelon Right anyway) the problem is fixed.
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