Are there any sources that claim that Rambam didnt author the summarized sefer hamitzvos (מנין מצות הקצר)?
It's hard to prove a negative, but I haven't seen any. The list comes from the Rambam starting each section of Mishnah Torah with a list of the included commandments. The commentators seem to take for granted that he wrote them and ask/answer questions on them the same way they do the rest of Mishnah Torah. See the Frankel edition of Rambam for examples.