Somehow when I changed the permalink of wordpress to a custom permalink the pagination links are not the same as before. Wordpress or the theme are adding query parameters to the url which I don't like. I tried already some of the solutions that I have found on Google, but without any success.
My pagination link is like that: https://myurl.com/custom-permalink/page/2?q=custom-permalink%2F
And I need it simply like that: https://myurl.com/custom-permalink/page/2
Thankfully I found the solution through this post: https://wordpress.stackexchange.com/a/78553
I just needed to change the code a bit and now it works as expected and I get the pagination link like that: https://myurl.com/custom-permalink/page/2
Just paste the code into your functions.php and it should work. Maybe you also have to go to the permalink settings in wordpress and click again on "save changes" after u added the code.
The code:
add_filter( 'get_pagenum_link', 'wpse_78546_pagenum_link' );
function wpse_78546_pagenum_link( $link )
{
return preg_replace( '~/(\d+)/?~', '?page=\1', $link );
}