A friend of mine once claimed that Rav Yosef Caro didn't have access to Rambam's Sefer HaMitzvos. It's apparently evident from comments he makes in Beis Yosef and Kessef Mishnah. I was hoping to see some examples where this is evident.
Perhaps he meant to share the claim regarding a number of Rishonim.
There's a debate regarding if specific Rishonim such as the Samag, Maggid Mishneh, and Migdal Oz saw the Sefer HaMitzvot, as it wasn't translated from Arabic to Hebrew for some time. Later Acharonim culled lists of instances in which each of them cites the Sefer HaMitzvot to dispel those claims.
Regarding your friend's, claim, I wonder how tenable it is given R' Yosef Karo had all these Rishonim.
Also, a quick search on Bar Ilan for "ספר המצות" in Kesef Mishneh, Beit Yosef, and Avkat Rochel yield over a hundred results. True, some are for the ספר מצות גדול\קטן, there are a bunch that clearly are citing the Rambam in the sefer and in the shorashim.