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In Mesechta Shabbos 49b, there is an opinion that the 39 melachos correspond to the number of times that the word melachah (and its variants) appears in the Torah. Rabbeinu Chananel comments that there are 61 instances of the word melacha in the Torah, and then explains which of these are disregarded to arrive at the number stated by the Gemara. In his article "Concerning the 39 Melachos of the Torah" (HaDarom, Tishrei 5726 (1965), pp. 159-80), Rabbi Gettinger points out that the word melacha appears 65 times in the Torah, establishes that the Rabbeinu Chananel originally had the correct figure, and offers a novel explanation -- compelling in its simplicity -- for how the Rabbeinu Chananel came to be corrupted.
Shiurim on Mesechta Shabbos