The Rambam wrote his Sefer HaMitzvos as a polemic against the Bahag's selection of the 613 mitzvos (as is clear from reading his Shorashim). They have many disagreements, which the Rambam lays out in his work.
From what I can tell, they both count a mitzvah to recite the Shema (Rambam Aseh #10, Bahag Aseh #1).
In the Machon Yerushalayim edition of the Bahag's work, they conveniently cross reference the Rambam's corresponding mitzvah number in the Bahag's list. When the Bahag has a mitzvah that the Rambam leaves out, they have the reference as a dash.
For some reason they have a dash after the Bahag's mitzvah of reciting the Shema. Unless I'm missing something, they don't disagree. Is there room to say they disagree? Or is Machon Yerushalayim mistaken (or is this a typo)? See below for a screenshot (the first one listed).
One potential avenue for an answer is the Rambam counts a seperate mitzvah of the Unity of Hashem, and I don't think the Bahag lists it. Maybe the Bahag includes it in reciting the Shema, although I don't see how that is evident.
EDIT: After studying this version of the Bahag more, I realized that Machon Yerushalayim are relying heavily on the listing of the Bahag's mitzvos which was determined by Rav Avraham Shimon Traube, whose notes are on the bottom. He's the one who divided up the mitzvos (as there were no commas or periods in the original Bahag, and it's vague where to put them). He's also the one who cross-referenced the Rambam's Sefer HaMitzvos. An older (and freely available) version of his work can be found here, and you can see in the older version there's also a dash beside the mitzvah of Kriyas Shema. So this isn't a question on Machon Yerushalayim, but rather on Rav Traube's interpretation.
What's strange is Rav Traube doesn't provide any footnote, something he was careful to do when suggesting an innovative interpretation of the Bahag.