The first thing that you should do is add : use strict; use warnings to the code.
There are many errors past the runtime errors that you described. "use strict;" is important because it is a compile time "sanity check".

for (my $i=0; $i<=$chrsize{$chr}; $i++) { looks suspicious and may be an "off by one" error.
I couldn't figure out what this code is actually supposed to to in terms of an algorithm - just not enough context for me to do that.

use strict;
use warnings;

#initiate S for the whole genome
#chrboundst = chr start index
#chrbound = chr end index

my $k=0;
my @S=undef;
#open OUT, "> temp.0";
my %chrboundst;
my %index;  # correct?
my @fix;
my @score;
my %chrbound;
foreach my $chr (keys %chrsize) {
 $chrboundst{$chr}=$k;
 for (my $i=0; $i<=$chrsize{$chr}; $i++) {
     $index{$k}="$chr\t$i";
     $fix[$k]=1 if ($breakpoint{$chr}{$i}==1);  # line 132
     $score[$k]=$piRNA{$chr}{$i}-$penalty;
     $S[$k]=$S[$k-1]+$score[$k] if ($i>0);
     $S[$k]=$score[$k] if ($i==0);
     $S[$k]=0 if ($S[$k]<0 || $fix[$k]==1);  # line 136
     $k++;
     }
 $chrbound{$chr}=$k-1; # mark the chr end for recalculation
}

__END__
Global symbol "%chrsize" requires explicit package name (did you forge
+t to declare "my %chrsize"?) at line 16.
Global symbol "%chrsize" requires explicit package name (did you forge
+t to declare "my %chrsize"?) at line 18.
Global symbol "%breakpoint" requires explicit package name (did you fo
+rget to declare "my %breakpoint"?) at line 20.
Global symbol "%piRNA" requires explicit package name (did you forget 
+to declare "my %piRNA"?) at line 21.
Global symbol "$penalty" requires explicit package name (did you forge
+t to declare "my $penalty"?) at line 21.
Execution of aborted due to compilation errors.
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