Anyone remember Due South? It was a comedy crime drama about a Canadian Mountie trying to track down his father's killer.

It got cancelled, but the fans protested and it was rescued at the last minute. The problem was there were a couple of significant changes to the characters and the whole thing felt off, like it was in an alternative universe... except they quite clearly implied that it was the same one and they wrote at least one of the changes into the plot, contributing to the discomfort. They never explained the wolf clearly being different though.

A similar thing happened between seasons with a more obscure show called WPC 56 about a policewoman in 1950s England, but that was clearly due to budget cuts rather than outright cancellation.

Then there's Red Dwarf series VII, which proved that more money is not always a good thing. It was a hard left turn that upset a lot of fans.

... and I'm sure a lot of people will say the same about what's happened to and in Doctor Who over the decades the show's been running.