use strict;
use Data::Dump qw/dump/;
my %loco_data = <DATA>;
print dump \%loco_data;
__DATA__
123
234
345
456

#{
#  "123\n" => 234
#             ,
#  "345\n" => 456
#             ,
#}
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Also, you should at least use strict;; use warnings; and use diagnostics; will give you even more info.
For opening files it's better to use the 3-element open.
Is the code you posted a cut-n-paste? I don't see where $locodn is coming from, or why you'd need to chop it.
chomp is generally preferable to chop.
To increment variables: $linecnt1++ or $linecnt1 += $x.

#!/usr/bin/perl

use strict;

my $logfile  = '/tmp/WDL_Scan_0000.csv';
my $locofile = '/tmp/locos.txt';

my ($locodn, $loco_data);
my ($linecnt1, $linecnt2) = 0;

open( my $file_1, '<', $logfile) 
  or die "Error: Cannot open $logfile.";
my @loco_data = <$file_1>;
close( $file_1 );

open( my $file_2, '<', $locofile) 
  or die "Error: Cannot open $locofile.";

while ( <$file_2> ) {
  chop($locodn);

  my ($RR_Name, $Loco_no, $Event_Date, $Event_Time,
    $Event_Code, $Event_Duration,$Source_File ) = split( /,/ );

  chop($loco_data);
  chop($Loco_no);

  $linecnt1++ if grep { /\b$Loco_no\b/ } @loco_data;
  $linecnt2++;

  print "Rec: ",$linecnt2, " In: ",$linecnt1, "\r";
}

close( $file_2 );
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my ($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;
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matches.txt:

1
2
3
4
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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
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output:

Total records: 1, matches: 0
Total records: 2, matches: 1
Total records: 3, matches: 1
Total records: 4, matches: 2
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I prefer:

my %target_matches = map { chomp; $_,undef } <$MATCHFILE>;
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No need for @keys that way.

Note: untested.

Ah.

Thanks so much - this is going to work great. I have one other question. My source file just because of the way it is built - the $field1 value has leading spaces, how can I remove them on the fly?

Source Example:

sx, 8849, sample1, source2
st,  893, sample2, source3

Matching Table:
8849
893
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With the leading white space the match does not hit. Thanks Again, Ad.