If you are seeing unwanted line numbers in code samples, you can turn them off by selecting "Writing" in the Book Tools menu for your book (https://leanpub.com/YOURBOOK/theme for the YOURBOOK in question), and then selecting "Book Theme".
If you then choose "Custom", you can choose to turn off line numbers on code samples (make sure to click the blue button at the bottom of the page to save the change). The next time you create a Preview, you should not see the line numbers anymore.
Please note that if you have read the Markua documentation you may have seen a description of a line numbers attribute on individual code samples. We haven't updated Leanpub to handle this Markua attribute yet, so it's still all-or-nothing via this setting.
Finally, please note that the Custom theme option is for Standard and Pro plans only, not the Free plan. To see your plan and change it, go here: