WP_User_Query counter not updating with pagination

You can try:

$number = $counter + ( $current_page - 1 ) * $users_per_page; 

with your increasing $counter variable in the loop.

Here we assume $counter >= 0, $current_page >= 1 and $users_per_page >= 1.

We might combine it into:

$number = ++$counter + ( $current_page - 1 ) * $users_per_page; 

with $counter = 0 as initial condition.