Christina,
Transition rules should be defined on the stream you want to pull leads into. For instance, say you have 3 streams (Early, Mid, Late). If you want to set up rules for leads to move to the Mid stream, you would create the transition rule in the Mid stream. This is why the filter does not allow for lead's already a member of Mid stream to enter the transition rule (because they are already members).
More information here: https://community.marketo.com/MarketoArticle?id=kA050000000LAXWCA4
Hope this clears up any confusion!