When using TaxJar with WooCommerce Subscriptions, taxes can get calculated for free trials.
We will work on getting this fixed. In the mean time use this snippet to counter the behaviour:
remove_action( 'woocommerce_calculate_totals', array( $this, 'use_taxjar_total' ), 20 );
add_action( 'woocommerce_calculate_totals', array( $this, 'use_taxjar_total' ),5 );