The Rambam writes in shoresh 12 of sefer hamitzvos that a single mitzvah may have multiple sub-part commandments, but these should be treated as part of the larger unit and not counted independently. Among the Rambam’s examples are giving reishit hageiz to a kohein or ma’aser to a levi – the separation of the geiz or ma’aser or other matnos kehuna that require hafrasha and the giving of these gifts to the kohein or levi are not separate mitzvos, but are sub-parts of the same mitzvah. The Ramban takes issue with the Rambam’s examples and distinguishes between two types of mitzvos: cases where an item becomes tevel and cannot be eaten before hafrasha is done, e.g. challah, and cases where a gift must be given to a kohein but there is no issur on the food before the gift is seperared, e.g zero’a, lechayayim, and keibah. In the latter case, the hafrasha and nesina are one and the same mitzvah of delivering gifts to the kohein. But with respect to challah, since the dough is tevel until challah is taken, there are actually two mitzvos: (1) hafrasha to be matir the dough; (2) nesina to the kohein.
One of the proofs of the Ramban is from the bracha of hafrasha. A bracha is normally recited on the gmar mitzvah, the completion of a mitzvah act – e.g. (Ramban’s example) we do not say a bracha on writing tefillin, only on putting them on. If the nesina to the kohein was the end goal of the mitzvah of challah, then the bracha should be recited when the dough is given to the kohein. Since we say the bracha at the time of hafrasha, it proves that this step is an independent mitzvah. (It also sounds like the bracha is on removing the issur tevel, an issue raised yesterday). Perhaps the Rambam accepts the Ramban’s notion of hafrasha being independently significant with respect to its being mechayeiv a bracha, but with respect to the count of mitzvos it is still subsumed under the overall unit of challah.
See here where we discussed Tosfos’ question (Pesachim 32): how is one yotzei terumah m’doraysa by separating one stalk of wheat when the Torah defines nesina as not less than a shaveh perutah? Obviously according to Ramban one can distinguish between hafrasha, which may not have a shiur, and nesina, which requires shaveh perutah.