$seen = [];
$i = 0;
foreach ($array as $data) {
    $number = $data['number'];
    $a = $data['values']['a'];
    $b = $data['values']['b'];

    if (isset($seen[$number])) {
        $output[$seen[$number]]['values']['a'] += $a;
        $output[$seen[$number]]['values']['b'] += $b;
    } else {
        $output[] = $data;
        $seen[$number] = $i; 
    }
    $i++;
}

checking result

print_r($output);

gives me this

Array ( [0] => Array ( [number] => 1 [values] => Array ( [a] => 1 [b] => 2 ) ) [1] => Array ( [number] => 2 [values] => Array ( [a] => 6 [b] => 6 ) ) [2] => Array ( [number] => 3 [values] => Array ( [a] => 2 [b] => 4 ) ) )