Rabbi Abraham Danzig writes:
והזהירה התורה על שמירת השבת י"ב פעמים, The Torah warns us twelve times about observing the Shabbos.
Does anyone happen to know where those twelve places are?
Thanks to @Meir, I found that the Rambam in Sefer HaMitzvos Shoresh § 9 brings this concept. In the Shabsi Frankel edition they list the following twelve places:
After checking out the Rav Kapach edition of Sefer HaMitzvos, I found he has the exact same list. I assume Shabsi Frankel got it from him. Rav Kapach doesn't provide a source for his list, nor does he cross reference an earlier source for the Rambam's count. I assume then that the Rambam is the originator of this counting.