This is a feature, not a bug. All prototypes were intended to retain their original color to distinguish them from regular robots, because some of them use the same sprite/ASCII as non-prototype variants of the same class.
However, that part of the design overlooked the fact that some players would actually get these things on their side while still potentially encountering hostile versions of the same. So I've already changed this behavior for Alpha 13--the color representing controllable allies will always override even the prototype default color (did it yesterday, in fact
).
