Collections, being data blocks that can reside inside other collections, can sometime end up in the ether and users don't know what's happening. Either by accident, or by opening and old 2.7 file with groups, etc... Currently you need to open a second outliner, switch it to Orphan data, and Drag and Drop the unlinked objects and collections to link them to your Scene collection.

Sometimes proposals come out as condescending but I know developers are aware of this and working on solutions, and I thank them for their work. This is just my proposal.

Proposal

• Expand the list by making a distinct part for unlinked collections and objects, bellow the hierarchy of the scene collection (the icon and the color are just for illustration purposes, the point is that it should be easier to notice)
• Make a toggle inside the Filter popover to view or hide this area, which sometimes you don't want to see
• Fix this bug or odd behaviour where, when you go to Object properties and delete all the collections from an object, the object becomes unlinked and disappears from your viewport. I think by default it should move directly inside the Scene collection instead