I also noticed this phenomenon and just assumed it was related to high costs. After seeing your question, I played around with various units in the Workshop (and using the Scenario Editor to "discover" advanced techs).
What I found was that the red text and exclamation marks seem to point out that you are designing a units with too many advanced features. As pointed out in the CUSTOM UNITS section of the manual, the cost factors are not additive.
For example, I designed the folowing unit:
Speeder Chassis
Fusion Laser Weapon (10)
Synthmetal Armor (2)
The workshop showed:
Cost 120!
Prototype Cost 180!
Then I designed another unit:
Infantry Chassis
Fusion Laser Weapon (10)
Antimatter Plate Armor (10)
Now the workshop showed, with no color or exclams:
Cost 160
Prototype Cost 240
So, even though the second unit cost more it wasn't highlighted. My guess is that you only get the highlighting when you design units with advanced chassis, armor and weapon. I didn't experiment with reactors or special abilities, though.
Interesting question!
Petek