Have any Jews ever denied that Moses wrote the entire Torah?

Individual rabbis and lay Jews throughout Jewish history pointed out that the truth could not be so simple. For instance, Rabbi Judah ben Ilai held that the final verses of the Torah must have been written by Joshua. [Bava Batra 15a, Menachot 30a, and Midrash Sifrei 357.]

Significantly, the Midrash still retains evidence of the redactional period during which Ezra redacted and canonized the text of the Torah as we know it today. A rabbinic tradition states that at this time (440 B.C.E.) the text of the Torah was edited by Ezra, and there were ten places in the Torah where he was uncertain as to how to fix the text; these passages were marked them with special punctuation marks called the eser nekudot. (5)

The Talmud [Shabbat 115b] states that a peculiar section in Numbers 10:35-36, surrounded by inverted nuns, in fact is a separate book. On this verse Midrash Mishle states that "These two verses stem from an independent book which existed, but was suppressed!" Another, possibly earlier, midrash [Ta'ame Haserot Viyterot] states that this section of the Torah actually comes from the book of prophecy of Eldad and Medad. (3).

In the middle ages, R. Ibn Ezra and others noted that there were several places in the Torah which could not have been written in Moses's lifetime. For example, see Ibn Ezra's comments on Genesis 12:6, 22;14, Deut 1:2, 3:11 and 34:1,6. Ibn Ezra's comments were elucidated by Rabbi Joseph Bonfils supercommentary on Ibn Ezra's work. (2)

In the twelfth century, the commentator R. Joseph ben Isaac, the Bekhor Shor, noted that a number of wilderness narratives in Exodus and Numbers duplicate each other, in particular, the incidents of water from the rock, and the stories about manna and the quail. He deduced from this that both of these incidents actually happened once, but that parallel traditions about these events eventually developed, both of which made their way into the Torah. In his words "The two are one!". (6)

In the 13th century, R. Hezekiah ben Manoah (known as the Hizkuni) noticed the same textual anomalies that Ibn Ezra noted; thus R. Hezekiah's commentary on Genesis 12:6 notes that this section "is written from the perspective of the future!", i.e. not from the ancient time of Moses.

In the 15th century, Rabbi Yosef Bonfils explicitly discussed the comments of Ibn Ezra, noting: "Thus it would seem that Moses did not write this word here, but Joshua or some other prophet wrote it. Since we believe in the prophetic tradition, what possible difference can it make whether Moses wrote this or some other prophet did, since the words of all of them are true and prophetic?"