split will separate your input line based upon the input keyword (such as SELECT). If SELECT appears more than once in the line, then the @things array will have more than one element, and you will get your message output.

#!/usr/bin/perl

use warnings;
use strict;

#This is where we read in the arguments from the command line
my $file_name = shift;
my $String    = shift;

#This is where we read in the file and output to the file
open(INFILE, $file_name) or die "Can't open file\n";

#while reading from the file...
while (<INFILE>) {
    $_ = uc();
    my @things = split(/$String/);
    if ($#things > 0) {
        print "There is a nested SQL in this file\n";
        exit;
    }
}
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