Hey there. I bought Endless Space a while back, and started getting into it recently. I read on the wiki that engine module bonuses stack, and so you can use them to gather a bunch of low level ships and use them to explore at seemingly "broken" speeds, and that doing this is called flocking. My question is: is this a bug or an exploit that be fixed later (or that was fixed already) or is it an intended feature that a player is supposed to use to boost his ships' speed? And will the AI use flocking as well?

It can be a surprise, but several ship modules offer bonuses "per fleet". This allows flocking. For example, an early engine module in the east tech tree gives +2 movement to ship, +1 to fleet. So a fleet of 9 ships gets +11 (two on its own plus one per member of the fleet). Search "tachyon" in the forum for a design where the ship's movement is 92. The AI "cannot help" using this, any ship with the engine will get this benefit. The same thing applies to other modules, such as repair modules and a high level weapon module.

so once you have these modules there really isn't much sense in sending lone ships to explore, right? considering you'll get a much better speeds if you gather them all together.

Well, sending a lone ship to explore costs less, since you are only building one ship.