It looks as if a filter-by-period setting returns records that are not linked to any time period at all. Since filter-by-entity works the same way for all entity types (places, periods, people) this must be a general bug. Try to find reproducable example and fix!
Note: seems to be a client-side navigation issue rather than a problem with the query, as initially thought. The 'referencing' filter seems to get lost in the UI as soon an item is selected.
It looks as if a filter-by-period setting returns records that are not linked to any time period at all. Since filter-by-entity works the same way for all entity types (places, periods, people) this must be a general bug. Try to find reproducable example and fix!