It seems to really be a bug... tho the explanation is easy.
The game prefers flat damage (you correctly guessed what that one does) over percentage damage - so if two units, one with percentage and the other with flat damage stand one nearby the other, the flat damage is applied to both. It may be that both use same field for the bonus in Object Editor and the game prefers higher bonus over "weaker" one...and flat damage usually uses higher number (comparing 3 flat damage and 30% in numbers is actually comparing number 3 and number 0.3... since 3 > 0.3, game chooses flat damage).
The bug is that the flat damage is still taken as percentage damage for one of those units.
Let's take an example:
Priestess of Moon: Basic damage is 34-44. She has Trueshot Aura that increases damage by 0.1 (percent damage), thus 10%.
Next unit is custom unit... let's say Archer with base damage 10-17. This archer has custom Trueshot aura that increases damage by 4 (flat damage).
When they come one to another, the Archer's Trueshot aura "beats" Priestess's one, because Archer's aura gives flat damage.
So archer's damage is 10-17 +4.
Now priestess's damage is 34-44 +156.
The reason for the +156 is that her aura, that increases damage by percentage, takes the value given by archer's flat damage aura as the percentage!
Basically, the default value for Priestess is 0.1 (10%), but with the archer close by, it changes to 4 -> 4 is archer's aura flat damage bonus, but for priestess it means 400%.
Since her damage is 34-44, the average damage is (34+44)/2 = 39 damage and 39 * 4 is 156.
Additional note:
Any other unit, which does not have the Trueshot aura with percents, gets flat damage bonus only.
