This may not be the solution you're looking for, but you could turn the problem around. Instead of populating the lists, use the numbers as keys of a hash and the lists as the hash values. For example:

# 13 is in list 1
# 23 is in list 5 and 6
# 42 is in list 1,3 and 5

my %lists;
@lists{13,23,42}=([1],[5,6],[1,3,4]);

# Find which lists contain the values
for my $i (13,23,42) {
  print "Value $i found in list $_\n" foreach (@{$lists{$i}})
}
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If you've already got the lists as arrays (or an array of arrays) this is probably not worth doing unless you need to find multiple values.

Perhaps more importantly the solution should make sense in the context of your code (which is hard to tell from your description), otherwise my solution makes the code harder to read/maintain and a different solution would be preferable, albeit slightly slower (since you need to search through all the lists).