I have a Morkie & this happened to her too. In fact, he skin darkened in so many splotchy areas that she kind of looked like a cow under her hair. Her name is Momo & we called her "Moo Moo".
It is normal with certain breeds of dogs. It hasn't happened to my purebred Yorkies, but Maltese have things called "black points" around the eyes, ears, nose, mouth & paws where the skin pigment turns black. Other areas, like the tummy, thighs or back can become grey or blueish. It is completely normal (even desired when showing Maltese) & the pigment tends to fade in and out in phases. They do get darker in the sun as well. You could visit your vet if it makes you more comfortable, but I wouldn't worry too much.