By default, the Wp-PageNavi plugin creates 2 pagination links, from the second page onwards - one at the top, and another at the bottom of the page. How can I disable the pagination at the top, keeping only the pagination at the bottom?
You have to edit your theme.
If you can paste the code of the page in question, i can tell you which part to remove.
if you found something like
have a backup first ;)
Check the plugin settings, but likely it is theme that has call to plugin's function in template or adds it to hook.