Content in your PDF will appear off-center when the Inside Margin is different than the Outside Margin:

This is expected, and typical for a book printed using print-on-demand: the larger Inside Margin accounts for visible space lost when your book is bound.
Viewing Your PDF
Because these margins are different, you may notice content shifting back and forth as you go from a page on the left side of a spread to a page on the right.
When proofing your print edition, then, it’s best to view your content a spread at a time. Open your PDF in the Preview utility that comes with your Mac. Then, use View ▸ Two Pages:

You can learn more about Proofing Your Book in Vellum Help.
Still have questions? Contact us.