Your second regex never matches which is why both are the same. As stated, here's a potential solution.

use strict;
use warnings;
use Test::More tests => 2;

my $content = 'BOGUS PPI3_SYNY3 276 aa linear BCT 13-NOV-2019';

$content =~ /^(BOGUS\s+\S+)/;
is $1, 'BOGUS PPI3_SYNY3';

$content =~ /(\d+\s\w+) linear/;
is $1, '276 aa';
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