Shalom,

The Gemara itself addresses and elaborates on your question. The simple answer is that the Mishnah is coming to teach that in the cases subsequently listed there, two are Torah based, and two are Rabbinical prohibitions. One difference between these two categories is manifest in the liability for each one's violation. For example, if one accidentally carried into a different domain on Shabbos (he forgot either that it is Shabbos, or that the act that he is performing is prohibited), he must bring a sin-offering for a Torah prohibition, whereas he is exempt if it was a Rabbinical prohibition.

Another difference is that in order to transgress the Torah law, one must pick up the object that is being carried, transfer it from one domain to the other, and then put it down. If one has not performed all three actions, at most he transgresses a Rabbinical prohibition.

B'Virchas Kol Tuv,

Eliezer Chrysler