By not pushing $in[0] on the @concat array. And to add an extra push after the loop:

sub concat
{
    my  ($aref,$slen)= @_;

    my @concat;
    foreach  my $i ( 1 ..  $#{$aref} )
    {
        my @out =  split (" ", $aref->[$i-1]);
        my @in  =  split (" ", $aref->[$i]);

        # value to be put in (intercepted)
        my $val = $in[1]-$out[1]-$slen;

        push @concat, ($out[0],$val);
    }
    push @concat, ($aref->[-1]=~/\S+/g)[0];

    print Dumper \@concat ;

    return ;
}
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