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I have been noticed unique behavior between virtual desktops on my Macbook. For example, Mail is in Space 1, my browser in Space 2, and Autocad in Space 3. Seemingly at random intervals, it will change Space 2 and Space 3, so I end up with, basically Space 1, 3, 2 (but they are labeled space 1, 2, 3).

Is this a feature, or something that can be fixed?

I'm not sure if it is related to the question, but I have also noticed that sometimes when I do the four finger swipe to change spaces, it jumps two spaces.

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The post apple.stackexchange.com/questions/74274/… might also be helpful to people experiencing this problem –  Daniel Lawson Dec 10 '12 at 14:51
    
HOWTO Arrange Desktop 1: I found out that the top menu placement in "System Preferences" -> "Displays" (upl.io/tor71u) also assigns the first set of spaces (Desktop 1+). So you can always assume the display with the "top menu" placement in system preferences to have Desktop 1+. –  dezza Jan 22 at 10:13
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My observation is that the "spaces" (now called "desktops") in Mountain Lion are sorted in a "most recently used" type order. That is, the more often a switch to a particular desktop, the closer to the "front" of the desktop list it is moved. If you enable the 4-finger "swipe up" Mission Control gesture, you can see the desktops in their "swipe" order.

I suspect one reason for this is that "full screen" apps get their own desktop, so the number of desktops varies dynamically, and the simple number/grid scheme from earlier OS X versions no longer can apply.

I tend to switch apps with command-tab, so the absolute placement of desktops is not so relevant to me. I do occasionally miss the ability to switch to a particular desktop with control-number, but have gotten used to using "swipe up" to find and select the desktop I want.

If you want to associate an app with a desktop of its own, switch to the "last" (empty) desktop, start the app, and select Options->Assign to This Desktop from the context menu in the dock for that app. If the app supports full screen mode, simply switch it to full screen and it will create its own desktop.

I was going to include a sample "Mission Control" screenshot below, but I haven't answered enough questions here yet, so I've posted it on dropbox instead. You can use the 4-finger left/right swipe to switch desktops in this view, or you can click on the thumbnail of the desktop you want to switch to. Across the top of the screen are the desktop thumbnails. Spotify is in full-screen mode. Desktop 4 has no apps on it. If I put an app there, I will get a new empty Desktop 5. I'm currently on Desktop 1, which is shown "exploded" below the thumbnails.

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Wow - great, thorough answer! I was beginning to wonder if it sorted the desktops per which are most used. Thanks for the explanation. –  bassplayer7 Nov 28 '12 at 1:49
    
Argh this is so frustrating, I'd rather just have consistency. Apple really has destroyed Spaces since Snow Leopard :( –  powerj1984 Jul 8 '13 at 18:03
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You can uncheck "Automatically rearrange spaces based on most recent use" on the "Mission Control" tab in system preferences. This will leave the desktops in the expected order.

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Excellent! - I think this answer is at least as helpful as the longer earlier one: The other answer gives more general explanations, but this fixes the problem - at least for me. Thanks. –  halloleo Apr 20 '13 at 4:25
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