Ghost lineages problem

The mainstream opinion is that birds developed from dinosaurs. But in the cladogram of that, all the sister taxa require ghost lineages. This does not seem to bother dino to bird people, but here is a problem. 

The "sister taxa" fossils appear after (closer to today than) the first birds, but folks think that the fossils that would fill the ghost lineage simply have not yet been found. 
However if the found taxa that are considered "sister taxa" are actually secondarily flightless birds, then that would explain them. And their timing would be consistent. The lineage would be quite different (than the current mainstream thinking) and there would be no need for assumed ghost lineages.

It shows that we need to be cautious about a purported lineage that requires ghost lineages, because the real explanation may be quite different.