Can you dye the costumes

To be able to perform a double assassination, you have to be in High Profile. Low Profile kills will generally allow you to kill a single target. It's not automatic like it was in previous games. But it ultimately depends on the weapons used. But in the end, it all depends on if two enemies are highlighted and not just one.

With the (Double) Hidden Blade equipped, when two enemies are close to each other and you are in range of both of them, you must enter high profile and assassinate them. If you are on a higher elevation, it will almost always do a double aerial assassination.

If you are carrying a (loaded) rifle, you can kill two enemies if they are lined up one behind the other. It doesn't matter if you stay in high or low profile for this, you'll be firing a shot and that is always a high profile move.

I don't believe there are other weapons that can kill multiple enemies in a single attack.

I encountered this once on the PS3 version. Rebooting my system solved it for me. I'm not sure how saving on the PC version works--you might want to try leaving the sewers, saving, rebooting, then going back into the sewers to see if that fixes it.