Recently I had a bug where using a cloak spell would dismiss my flame atronach. Im to low level right now to test it on other summons and I dont think ive had this problem before. Is this a issue caused by dawnguard or the newest patch?

There have been reports of this happening, exactly the way you put it, on dead thralls. It's probably the same bug.

I've had the same issue. I get around it by summoning before I put the cloak on.

Typically, a mage needs to start a fight with an illusion spell and a summon spell before even entering battle. However, if your summon(s) take care of the fighters, then there's no need for the cloak spell anyway.