There's actually no way to delete any versions currently.
We use a version control system called Git, and we just make a new commit every time you preview or publish. These versions of your manuscript are just for your use, and they're not shown to anyone. (By the way, we don't actually store the generated versions of your book each time. We just store the manuscript.)
If you know Git, then you may be thinking that we could allow you to delete versions, and you'd be right. However, that would enable less-technical authors to make a mistake and lose work, so we just don't provide the feature on purpose.
Someday we'll probably paginate the Versions page or provide filtering options or something. But for now, my advice is to just ignore it, and take comfort in the knowledge that we try to help ensure you can't lose your work...