pagination-mod.php

<?php

	$data = Timber::get_context();
	$paged = (get_query_var('paged')) ? get_query_var('paged') : 1;
	query_posts('posts_per_page=2&paged='.$paged);
	$posts = Timber::get_posts();
	$data['posts'] = $posts;
	$data['pagination'] = Timber::get_pagination();
	Timber::render('date.twig', $data);

So get_pagination() relies on using the current query. Even though you're sending new data to Timber::get_posts(); the original query is unaffected.

To modify that query you just need to send query_posts the new info (which modifies the WP loop). In a future release I'll make it so this happens automatically.