@a puts $s1 =~ /(\d{2})/g in list context so all matches will be found and used to populate @a. You probably want something like:
#!/usr/bin/perl
use warnings;
use strict;
my $s1 = "45 20 00 00 00 03 00";
my $s2 = "40 20 00 00 00 00 00";
my @a1 = $s1 =~ /(\d{2})/g;
my @a2 = $s2 =~ /(\d{2})/g;
die "Mismatched lists" if @a1 != @a2;
print "found $a1[$_] and $a2[$_]\n" for 0 .. $#a1;
Prints:
found 45 and 40
found 20 and 20
found 00 and 00
found 00 and 00
found 00 and 00
found 03 and 00
found 00 and 00
True laziness is hard work
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