A common mistake is to

a) Create a custom filter
b) Select, say Custom Object, as the metadata object
c) Refine the filter by choosing to select only some custom objects

BUT - either change mind and click out of the dialog or , simply never choose any item(s)

So, even if you (in the left hand pane) ticked Custom Object, if the Named items is an empty list, you'll get no custom objects in the compare

In other words, if Named Items is the state of the filter but no items were named, that is a nonsensical configuration and user should be warned