How are you guys trying to reproduce it?
Technically speaking, what's in the OP is what's supposed to happen. IC made it so that in a mixed fleet (it has to be a fleet), support ships like Cielos, Hoshikos, Subverters, Subjugators, etc ignore direct attack orders - this was after many complaints from beta that people wished the support ships wouldn't attack and instead focus on what they do best (repair, disable, etc) because while attacking they don't do anything else while the target exists.
So, IC changed it so that the support ships do not obey direct attack orders unless they are the only selection. So if you select a fleet of 10 Hoshikos and show them to attack, they will. If you select a fleet of 10 Hoshikos and 20 Cobalts and show the fleet to attack, only the Cobalts should.
This does have the side effect described in the OP, that if the fleet had previous movement orders and you show it to attack without cancelling the move, the support ships will finish the move order, even if it's a jump, and then try to reunite with the fleet.
Note, I have not actually tried it myself in 1.09, but I have definitely had it happen, and posted about myself