This is a bug in Mutter or Gala, reported at Launchpad.
Feel free to add more details and track the issue there.
You did not state if these windows opened up that way ... or if you did something to make them that way.
Since I am at work right now I cannot test this out ... but ... did you try to double-click the title bar?
My recollection is that the first double-click will maximize the window and the second double-click will resize it back to its default opening size.