my ($linecnt1, $linecnt2) = 0;

Is that what you meant to write?

linecnt1++ if grep { /\b$Loco_no\b/ } @loco_data;

Doing a hash lookup--like the op was trying to do--is more efficient than searching the entire array every time through the loop. You know, O(n squared) v. O(n) type stuff.

use strict;
use warnings;
use 5.010;

open (my $LOGFILE, "<", "logfile.txt");
open (my $MATCHFILE, "<", "matches.txt");

chomp(my @keys = <$MATCHFILE>);
close $MATCHFILE;

#Initialize hash:
my %target_matches;
@target_matches{@keys} = ();
#now the keys exist, and the values are undef

my($num_records, $match_count)  = (0, 0);

while (<$LOGFILE>) {
    chomp;
    my @fields = split /,/;

    if (exists $target_matches{$fields[1]}) {
        $match_count++;
    }

    $num_records++;

    say "Total records: $num_records, matches: $match_count";
}

close $LOGFILE;
[download]

matches.txt:

1
2
3
4
[download]

logfile.txt:

a,5,b,c,d,e
a,2,b,c,d,e
a,8,b,c,d,e
a,3,b,c,d,e
[download]

output:

Total records: 1, matches: 0
Total records: 2, matches: 1
Total records: 3, matches: 1
Total records: 4, matches: 2
[download]