There are two common reasons that your track will be listed as "album only" on iTunes.
The most common is that your track is longer than 10 minutes in length. Any track that is longer than 10 minutes will automatically be listed as "album only" on iTunes.
The second possible reason is that your label already has the track in question for sale on a separate release. If iTunes detect this then they will put the new occurrence of the track as album only and go on the assumption that users searching for the track will buy it off your other release.
As frustrating as this is, unfortunately, nothing can be done to reverse Apple's decision to mark your track as "album only".