In Freeciv, all human players move concurrently, during the same turn. It was always this way; trying to make this work was the reason for creating it.
AI players were added later. Human and AI players do take turns: AI players never do anything during a turn, they only act at the start and end of a turn. They are a lot easier to implement that way. But the difference has been confusing novice players ever since AI players existed.
You could have looked this up in the manual. My guess is that instead you played a few games on your own, against AI players, then got your big cold shower in the first game where a fellow human player approached you in battle. I'm not sure what you were expecting; you must have been aware that human players were moving concurrently, so why did you expect things to somehow be different in battle? But I think I was just as confused as you about the game mechanics after my first Freeciv games against other humans. It was a pretty rough experience. (And it still is. I never got good at it.)
So your experience isn't exactly unique. And you're not exactly unique in wanting human players to take turns, either. What is unique is your conclusion that Freeciv changed between the games you played against AI and the games you played against humans and dropped being turn-based. It did no such thing. As a matter of fact, it did exactly the opposite: in 2.2, and option was finally added that requires human players to take turns. You could have found that in the manual, too: phasemode.
The problem is that Wikipedia editors require "published" references, which typically means "published on paper" - which is a crazy criterion for software.
Mirrors should reflect a little before throwing back images. -- Jean Cocteau