Potential cause to "best of gen" problem is that You probably store reference to "best entity" (or shallow copy, instead of deep one) and then modify it by mistake. Second problem i encountered is that used evolution algorithm sometimes regresses in fitness, possibly because its "too static" (meaning there are problems with discovering other potential solutions and/or its stuck in local minima).
I only store the brain of the best creature in its chromosome representation, i.e as a string, which is an immutable object in C#, so there is no way for me to accidentally modify it without replacing the whole thing. On top of that, I have also already tested and confirmed that the creature in the "best of"-screen always has the exact same brain it had during the simulation.
In theory, the fitness should never decrease if the "keep the best creature" setting is turned on, but yes, I have also seen this happen. I currently attribute both of these problems to the fact that Unity's physics system (which the whole simulation is based on) depends quite a lot on random external variables - such as frame rate drops - and given its approximative nature isn't as deterministic as it should be.
I'm trying to optimize the performance as much as I possibly can for the next update in order to get rid of any potential performance spikes that might interfere with the physics system. I unfortunately can't change the physics system itself so there is a certain performance limit that I can possibly optimize to. If you create tons of creatures with a bunch of body parts each, the physics system is by far the main reason for the extreme lag that you will see, and there's pretty much nothing I can do about that, which sucks. I can't even hardware-accelerate it, even though the fact that none of the creatures collide with each other is a perfect basis to parallelize those physics calculations on the GPU.