If we create an inventory file like this:

[simple]
host1

[complex:children]
simple

[complex]
host2

and then we run this script

import ansible.inventory
inv = ansible.inventory.Inventory('inventory_file')
total = set(inv.get_hosts())
allgroup = inv.get_group('all')
all = set(allgroup.get_hosts())
odd = list(total.difference(all))[0]
print odd.name

We will see that 'host2' is not included in the 'all' group.

If we change the inventory file to be

[simple]
host1

[complex]
host2

[complex:children]
simple

then it all works.

I'm not sure where the bug is, but it was very confusing when I was trying to see if the variables from group_vars/all we're being picked up correctly.