There's nothing wrong with your comparison if ($array[$i] eq '['); rather, I'm guessing it's a problem with the way you're iterating over the array, and trying to change it in-place.

I would recommend you use a temporary array for this, as it's easier to process, and there's no chance of messing up the original:

#!/usr/local/bin/perl 

use strict; 
use warnings;

use Data::Dumper;

my @array   = ('A','B','C','[','D',']','E','F');
my @results = ( );

while (@array) {
    my $string = shift @array;
    if ($string eq '[' and @array > 2) {
        $string .= (join "", splice(@array, 0, 2));
    }
    push @results, $string;
}

printf "Results => %s\n", Dumper(\@results);
[download]