by default, critical CSS is inserted inline, whereas the "normal" CSS is deferred until after document load. as soon as the domcontentloaded-event fires, there is JS that will insert the links to the autoptimized CSS in the head as well and those will be downloaded. at that point you will indeed have two sets of CSS; a part inline (used to style the page initially) and the normal external CSS (inserted by JS after the doc has loaded) which contains all styles.
so if that is what you're seeing; that's not an issue, it's by design. if you're seeing something else, you'll have to be a tad more specific (a URL helps, generally) :-)
frank