You should first store every 3 items to an array. Each value has 3 items. Then iterate the array to output row and popup.
Also you should keep ‘container’ out of loop.
<?php
$items = [];
if ( have_rows( 'content' ) ):
while ( have_rows( 'content' ) ): the_row();
//initiate if is not set
$items[ get_row_index() % 3 ] = $items[ get_row_index() % 3 ] ? $items[ get_row_index() % 3 ] : '';
$items[ get_row_index() % 3 ] .= '<div class="item">' . get_sub_field( 'name' ) . '</div>';
endwhile;
endif;
?>
<div class="container">
<?php foreach ( $items as $item ) {
echo '<div class="row">';
echo $item;
echo '</div>';
echo '<div class="popup">';
echo $item;
echo '</div>';
}
?>
</div>
