The Sefer Yereim by Rav Eliezer MiMitz is an important work on halacha. It's also a list of the 613 mitzvos, as that is how he organized this halachic work. What many do not know is he based his list on the one of the Bahag, with some differences (parenthetically, I noticed he lived at the same time as the Rambam. Maybe he didn't have the latter's Sefer HaMitzvos, and the Bahag's list was all he had to work with, rather than making his own).
If one were to look at the work, they'll notice that there are only 464 sections, not 613. The author himself addresses this in his introduction and says that sometimes he grouped together mitzvos that were related.
כי כל מצוות הנכללות בדמיון אחד אייחד לבד בכלל אחד.
He's more explicit at the end of his work:
וסיימתי מצות ותולדותיהן כאשר השגתי בעצת דעתי והשבתים כאשר מצאתים בספר רב יהודאי גאון ז"ל וכללתים בארבע מאות ששים וארבעה כי בכמה מקומות כללתי שתים כאחת.
I was wondering if anyone took the time to go through his sefer and indicate how many mitzvos are covered in each section. It would be nice to know if it actually came to 613, and to know how.