I'm having an issue since 1.1 where I will select a group of units and select an enemy unit for them to destroy, then zoom out and come back 5 minutes later and they have losted their targetting and are attacking everything but the target I selected. I lost far more cap ships then I care to admit because of this. This was never an issue prior to 1.1. It makes multitasking battle fleets across different planets quite discouraging.

I've run into something similar.   I will take a fleet and I will right click an attack order on a structure.  Then i'll hold down shift and right click to que up each successive building I want the fleet to destroy.  They get out of order often

I've noticed with fleets that when giving orders the flagship will carry out the order with the rest trying to form up instead of keeping pace. So when an attack order is given the flagship moves to attack position but the rest of the fleet won't really do anything until they have formed up on the flagship again, after that they seem to act like they should, such as attacking sturctures, enemy ships, bombing planets or w/e.

Considering how slow even frigs move in this game I can easily see how trying to 'form up' would make fleets do completely insane things when they get conflicting commands like 'attack this', so they try to form up, but while forming up a target comes into their engagement radius so they engage it and ignore the primary target entirely.  Since the capital does not move much, just re-orients, it does not suffer the same problems.

So... is there an 'open fleet' command where the ships are not fixed to their fleet formation and will move on the selected target by the most efficient means and engage that target once in range?

I haven't actually tried it, but I imagine setting the formation to "loose" would make it so the ships can engage targets sooner since it shouldn't take so much time to form up.