Another follow up to my earlier question:
"I have wondered about this for a long time. If you do a cladistic analysis and you do not include the actual ancestral group within the analysis, will the cladistic analysis alert you to that?
If so how does it alert you?"

Your answer that "many state transitions" would be an indicator is helpful. And you have confrmed that lengthy ghost lineages and numerous exaptations are also other indicators.

The reasons I have asked this, is because the dinosaur to bird theory has many state transitions, lengthy ghost lineages and numerous exaptations.
A veritable trifecta of indicators that indicate that the actual ancestral group may not have been included within the analysis. That dinosaurs may not actually be the ancestors of birds.

Has anyone made that observation about those three indicators and published anything about that?

"The reasons I have asked this, is because the dinosaur to bird theory has many state transitions, lengthy ghost lineages and numerous exaptations."

No it doesn't. Cladistic analysis that include modern birds and mesozoic theropods include big transitions, because of the big chronological gap. But analyses that include a good selection of ancient and modern birds as well as anceint theropods have nice, clean transitions of only a few characters each. The difficulty is drawing a line at any point and saying "the animals more derived that this, we will count as birds". There's no obvious place on the tree to do this, precisely because the transition is so smooth.