I deployed an app to the Windows Phone Store and the version number that got deployed is different than the version in the app manifest.
The version that got deployed is something like 2014.MMDD.ABC.XYZ
It should have been 1.0.0.0.
Why was the version number changed, and is it possible to change it to what it should be?
That is the version for your appxbundle, not for the app itself. The bundle contains the resources so only the relevant ones are installed on any specific devices. The app itself should still show up with the right version in the store.
If you look in Program Files/WindowsApps on your desktop you'll see the same thing there: many apps will have both the normal package and timestamp-versioned bundle packages.