I came across a similar issue with my ancestors. A lot of my ancestors wrote down on their naturalization documents the "governorate" where they were from in Russia as opposed to the city. Some may not have remembered and some "governorates" shared names with cities and other places. For example an ancestor of mine put down Podol/Padol on numerous documents. That was a "governorate" in Russia at the time and there were other cities/towns that shared that name, close and far.
In your case, Mohilev was a city in Russia and at the time and was in the "governorate" of Mohilev. Mohyliv-Podilskyi, at the time, was also a city in Russia, but in the "governorate" of Podolia. If I had to bet I would put my money that when your great-grandfather said he was a citizen of Mohilev, that he was referring to the "governorate" of Mohilev.
Happy New Year!