A time consuming process, right? Luckily, the situation right now leads us to believe that this very well might be a bug, or at least an oversight on Zynga's part. As there has been no official confirmation (as of this writing) that this is the way things were intended to function, we'll chalk it up to a bug and hope the development team fixes the issue. In the meantime, if you're looking to complete the Canning Master missions by selling off your excess adult animals for your Food supply, make sure you remove them from the Livestock Pen first, or selling them will be moot.
Have you experienced this issue in FrontierVille? Does the lack of Food from selling change your opinion about the Livestock Pen, or will you continue to use it as normal? Let us know in the comments.