Hi Vicky,
 
Bubble shells belong to a group of mollusks known as Opisthobranchs.
Most of them do not have a shell, but some, like the bubble shells,
do.  These animals are hermaphroditic (both sexes in the same
individual - self-fertilizing), and of those which have shells, most
are ovoviviparous (the fertilized eggs are retained in the parent's
body until they hatch).  So, the tiny shells you found inside the
bubble shells are embryonic, or newly hatched shells of the same
species.  The same can be found in some fresh water snails such as
the genus Viviparus. (I am making one assumption here - that your
reference to "cleaning bubble shells" means removing the soft body
parts from live-collected bubbles.  If you are talking about some
kind of tiny shells that you found inside of dead, empty bubble
shells, then there are many possibilities.).
 
Paul M.