It sounds like you might have one or two batches that were sent out but haven't come back – for instance, if you refreshed the browser or if the same session was accessed by multiple users. In the default setting and expecting that potentially multiple people access the same session, Prodigy can only know whether a batch is coming back at the end of the session. When you restart the server and any examples were missing, they should be queued up again.
Alternatively, if you want to always ensure that batches are sent out in the same order and that examples are re-sent if they haven't been annotated yet, you can set "force_stream_order": True. (In that scenario, you just have to make sure you don't have two people on the same session, as this can lead to duplicates.)