What do enemy colors mean?
During the Destruction sections of 13 Sentinels: Aegis Rim, enemies have been colored red, blue, and yellow. I've seen that the same enemy type can come in either red or blue. What do the different enemy colors mean?
The different colors (red, blue, and yellow) refer to the generation of that Kaiju. The ascending generations are stronger and have additional abilities.
I can't find an explicit source that says this outright, but you can check something like this guide to see how the three generations of the Twintail (along with pictures) are different.