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Thanks for the long answer. Game is very good despite those few problems. I'm enjoying it a lot and  looking forward to try next update.

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).