From the user manual:
"In a fleet battle, the attacking side adds together all of its attacks against a single defending ship, even if the defender is also a fleet (in which case the most lethal but most easily destroyed defending ship is targeted first) ".
It isn't very clear that if the defending ship is killed and not all attacking ships have fired, they will target another ship.

Manual says you need one Megaton of food for each miliion. I have a 10.98 billion planet that is producing 20mt and is still increasing. Manual should say 1 mt needed for each BILLION right?

I made this same point in the past. Some of the references suggest the population is measured in millions and others billions. Notice when you select a colony or troop transport ship it reports each module holding up to 500,000, and yet other references suggest the number is 500 million.

Page 57:

If you play as the humans, the AI gets an additional advantage - they know where all the planets are. Humans don't start...

It was explained this is now changed and nobody has any informations.

How about adding a table of keyboard shortcuts?

I found out purely by accident that pressing the 'C' key centers on the selected unit.

Here are some more errors that I discovered while I read through the draft:

p.12 Change the sentence "The forms of government are:" since you then proceed to list the different political parties.
And maybe put the Warparty last since all of the others are in alphabetic order.
p.28 "Colony is currently defended by ships and orbit and cannot be invaded". Shouldn't it be "in"?
p.55 "Orbital Terraformer: All potentially useable tiles your planets are instantly useable". Missing an "on".
p.55 Typo in description for Hyperion Fleet Manager. "oribtal".
p.56 Still no description for Orbital Planetary Fleet.

Otherwise, it looks imo very good, except for the Galaxy Size and Trade Goods lists but I'm sure you are already aware of that.

At the end of the manual a link is added to access an online tutorial. There are two things that would make it more useful:
1) Move the tutorial from online to into the manual. Perhaps with a link for updates.
2) At the least, move the link to the tutorial to the front of the manual. At the back it's buried, but at the front is where people first turn when they don't know what everything means.

In draft 3, page 48, it is described that a ship with 1d6 attack, 1d2 defense will lose almost every time against a ship with 1d4 attack, 1d4 defense. I disagree. With low hit points, first strike dominates and with high hit points, the 1d6/1d2 ship will usually win.

Uh, why? I think you may have missed the fact that Ship 1's defense is the wrong type, so his defense is square rooted. So it's more like 1d1.4 defense instead of 1d2 defense.