Most likely it is that you need to quote the BadShares interpolated string: m/(\Q$BadShares[$i]\E)/i. However, the code snippet you have given is not ameniable to us reproducing your error. Try plugging suitable data into:

use strict;
use warnings;

open tempFile, '>', "test.dat";
print tempFile <<TEMP;
it is always the last line). Line 23 is the pattern match part of the 
+code. If
is my early test script before I get it to go through a list of files 
+in a
TEMP
close tempFile;

my @BadShares = <DATA>;

# Open the file/s to remove these matches from
open CURRENTDAT, '<', "test.dat";
my @DatLines = <CURRENTDAT>;    

# For each line in the file to match from
for ($a = 0; $a < scalar(@DatLines); $a++) {
    # Go through each line of the file to remove these matches from
    
    for (my $i = 0; $i < scalar(@BadShares); $i++) {
        # If the current line in the DAT matches any line in the file 
+to match set
        # that line to zero
        if ($DatLines[$a] =~ m/(\Q$BadShares[$i]\E)/i) {    
            print "MATCH  $DatLines[$a]       $BadShares[$i]";
        }
    }
}

__DATA__
Line 8 is the last line in the file test.dat (this error changes if I 
+add lines
it is always the last line). Line 23 is the pattern match part of the 
+code. If
I print the lines as it goes it is less than half way through Bad_Shar
+es.TXT
and the line changes as I add lines to test.dat (running out of memory
+?). This
is my early test script before I get it to go through a list of files 
+in a
given directory (lots of DATs containing drives to map for specific us
+ers).
[download]

Prints:

MATCH  it is always the last line). Line 23 is the pattern match part 
+of the code. If
       it is always the last line). Line 23 is the pattern match part 
+of the code. If
MATCH  is my early test script before I get it to go through a list of
+ files in a
       is my early test script before I get it to go through a list of
+ files in a
[download]