I have encountered this quite a few time's now in LAN & Online games.
Mid-way through a seemingly long game (1-2hr's in) the game will de-sync without reporting it to us, yet the game will continue. Leaving us a little at a loss as to whats going on. It's as if the AI takes over for the other players yet we still stay connected & certain events happen on others' (but not all) people's clients.
Earlier today I was in a game and I had a starbase, fully upgraded (3x Health, 2x Weapons, 2x, Ship Production <I was TEC>) and my companion within the game asked me where my starbase was, he literally couldnt see it. He then asked if I could see his starbase (which he setup in the same system) of which I couldn't. He could see I had the system however he couldnt see my fleet, starbase, or culture generating building that was in the system, and I couldnt see his Starbase.
This has happened when we've been playing with mixtures of the factions so it doesnt seem faction specific, how ever I only ever play with friends against the AI so it may be a Player vs AI only bug. Whatever it is, it currently makes longer games nigh on impossible to complete and as such playing rather pointless.
This has also been reported here: http://forums.sinsofasolarempire.com/333953 however I thought id post it up in the correct place with a little more of a write up.
Love Entrenchment however it's a shame this bug is here as it cuts alot of would-be fantastic games short due to de-syncs.