The place to look for this is in Collected Writings of Rav S.R. Hirsch, the volume on Oral Law (I think Vol. 5 but I can't check it.)
The volume is divided into two parts.
The first part is a critique of H. Graetz's "History of the Jews" the volume discussing the evolution of the Oral Law.
The second part is a critique of Zechariah Frankel's "Darkei Mishna".
In both parts, Rav Hirsch quotes the authors citing various sources and drawing mistaken conclusions.
He then shows why their approaches are mistaken and brings proofs to that effect, and explains the correct understanding of the texts.
If you want a sampling of traditional sources which can be misunderstood to mean that there was a transition from "Temple Judaism" to "Rabbinic Judaism" check out the volume.
One example: Graetz builds a lot upon the assumption that Rabbi Yochanan Ben Zakkai came to do exactly this. In post-churban Judaism, RYbZ felt the need to shift the focus from the Beis Hamikdash to Torah study.
Graetz then brings a number of sources which could superficially be understood to mean this is what he did.
Rav Hirsch then quotes those sources in their context, shows how Graetz misinterpreted them, brings other sources to buttress his arguments, and then explains what RYbZ actually came to do.
And while it's a shame that both Graetz and Frankel were kofrim, they at least knew a lot. Thus they quote sources from all over the place- albeit improperly.
As a result, Rav Hirsch is literally bringing from all over Shas Bavli, Yerushalmi, Tosefta, masechtos ketanos and more in order to discuss and refute their claims.
Thus this work is the best one for anybody who wants to see authentic sources which could be misinterpreted, while also seeing the proper way to read them as well.