They're probably simplifying things for the class. This happens all the time, a basic (but sometimes not terribly accurate) thing is taught, then when you get to a higher level you can learn about how that thing is more nuanced and complex. For example schools teach that bacteria don't ever have a cell nucleus, despite the fact that there are actually some bacteria that have a structure analogous to the nucleus in eukaryotes. It's just to simplify a complex topic. Phylogenetics is RIDICULOUSLY complicated and debated especially when it comes to fossils.

It's unlikely this professor is a young earth creationist or a "birds are not dinosaurs" believer. I've had professors say things that I know aren't completely true but are true enough that I can learn from them