You should probably define $vecgcd. The following works:

use Bit::Vector;

my $veca = Bit::Vector->new_Bin(5,"00101"); # 5
my $vecb = Bit::Vector->new_Bin(5,"01010"); # 10
my $vecgcd = Bit::Vector->new(5); 

$vecgcd->GCD($veca,$vecb); # should be 5

print $vecgcd->to_Bin(); 
__END__
00101
[download]

Hope this helps.