Why does auto-attack or auto-retreat sometimes not work?

They seem to only work for the current situation you are in. For example, if you are attacking the Yor, and you put a bunch of your ships on auto-attack,, also taking into account you can see some Yor ships on your screen...then your own ships will go and attack them, and they will continue to do so until you can no longer see anymore Yor ships. Once you could no longer see any Yor ships, then your ships turn back to you for their next command, since there would no longer be anymore enemy ships left to destroy.

I have found this to happen a lot as well with survey ships. I'll put them on suto-survey, but once no more anomalies can be seen on the map, then your survey ship will turn back over to your command, despite that there could be hundreds of more anomalies out there. If it doesn't know they exist, then it can carry out the auto-task you assigned it.

~SDC~

I believe that Auto Attack and Auto Retreat only come into play when there are enemy ships in sensor range.

Yeah, auto-attack and survey will only target objects the player can see. If an anomaly or enemy ship is covered by the FOW, it wont go after it. Also, as Cari said, they both take range into account, so if your enemy has a fleet half way across the galaxy, those ships will be ignored by short-range fighters.

As for auto-retreat, I beleive the ship will dock at the closest home star when it's down to 20% of it's total HP. So if your ship is damaged but still at 7/20, it'll continue to fight.

~SDC~

Thank you, Governor. I wondered how auto-retreat actually worked.

Auto-attack is great when you have superior ships - fire and forget! Watch out for the occasional heavily defend SB tho.