Take the present fossil ostensibly under discussion here. Was that in fact an intermediary creature between species? I don't know, maybe. I do not see compelling evidence that we know for sure. I for one really have a hard time stating such things as facts with a straight face; I feel like I need to prepend phrases like "The fossil record suggests that".
Incidentally, I feel the same way about historical anthropology... statements like (making something up) "These ancient people wore fur hats and ate with their fingers out of stone bowls," based on some bowl fragment and a bit of fur found near the remains of a skull. Well, I don't know, maybe that was true! But such evidence seems weak to me, and hardly enough to present those ideas as facts.
And perhaps my gripe is more with mainstream media presentations and with loosely-written educational materials than with actual scientific research.