https://xcraft.net/battle/index.php?battle_id=37da54b7b992cb20db090067d7e6bad5

I attacked a pirate fleet, and according to the simulation I should win with at most 1 of my 10 cruisers lost, in reality I lost the majority of my fleet
It seems like the damage they do to me is very focused and fairly soon I start losing ships (and firepower) one after the other.
On the other hand it seems like the damage I do to them is very spread out, It took a significant amount of damage before the enemy started losing ships (and firepower), the enemy cruisers were at less than 25% health before they finally started giving in, so they were able to fire at me full strength for a lot longer than I was able to fire at them
Seems a fight where the enemy gets to use a better strategy then I do, or am I missing something?

The only useful order I have during battle is 'attack' on a group of ships, what the other 2 orders do I don't know (no mouse-over description available)
How do I give orders to focus attack on a single ship at a time as to lower the enemy strength as quick as possible?

On top of that 1 cruiser is now being repaired (and blocking my production queue unless I pay 1 hydarian crystal) for a whopping 12 days, while I can build a cruiser from scratch in 75 minutes
(Edit: just found out the repair queue is separate from the production queue, so atleast that doesn't block things)

Yes, they fight the same rules. All pirates have Admiral of level 10, which means that their armor, shields, and attack is 50% stronger. Did you consider this in your simulation?

Most players do not account for the different levels of simulation that can be as much as 50% off. In order to be mostly accurate, coach level 3, a premium officer must be purchased and then spend 1000 vespene a simulation, otherwise the results are badly off...
As a general rule, I double what no coach says I need to take no losses. With coach level 1 add 50% of the fleet, with coach 2 add 25% of the fleet, and coach 3 is mostly accurate but does not account things like scourge, or player issuing commands. So it can be a tiny bit off.
 
Tech levels do play a major part in things and even 2 levels difference can mean loosing a battle in an otherwise winnable battle. You need to pay attention to the techs... 
Pirates normally are level 12 on weapons / armor / shields, 10 on admiral, and then you have the various tech that apply by race such as laser / plasma, acid / metal spike, etc. These can range from 10-20 on some pirates and scene players. These apply from base ships so if you want to spend the time, you can calculate out what the real specs are on the various fleets you attack before hand but it is very time consuming.