I've played 1.04 a bit now and seen movement and attack orders randomly canceled, the result of which is that a ship will go off and do something else. For example, if you tell your siege cap to attack a planet, it will do so for awhile, but then for no apparent reason (and without giving orders to that ship or even any other ship in the same grav well), the siege cap will turn around and attack a nearby enemy frigate. The siege cap wasn't part of a fleet, auto attack was off, and auto join fleet was turned on but there were no fleets in the grav well.
Another example, a set of ships (not in a fleet, no other fleet in the grav well) would be all told to attack an enemy heavy frigate, then some ships (not all) would switch targets to a different enemy frigate before the first was destroyed.
Both my friend and I have seen this behavior repeatedly with our own ships. Games are usually 2 players vs 3 hard AI (aggressor, fortifier, researcher).
Unrelated, seems like with all the botched updates (people complaining about 1.04 crashing etc.) that you guys should leave the previous update online in case people need to revert. You know, a little link at the bottom of Downloads "click here for previous versions" or somesuch.