I learned German in Austria and I was taught a handful of words which we use a different article here as compared to in Germany. My recollection is that most of these words either were commercial, like Nutella, or loan words coming from other languages (e.g. not every loan word is neutral).
But while I did eventually get my C1, my German isn't great so I don't want to claim any expertise.
An example that comes to mind is butter. It's feminine (die Butter), but in some dialects, it's masculine (der Butter). There are maps for several other words at http://www.atlas-alltagssprache.de/runde-5/f15a-f/, but I'd take them with a grain of salt. The region I grew up in doesn't really match what these maps say about it.
Oh, I know certain people in Bavaria calling "das Butter", suspicious people no doubt! Everybody knows it is "die Butter" with an option to settle for "der Butter"!
Nutella is a pathological example. It's a running gag among German speakers that they cannot figure out its gender. The discussion usually ends when someone suggests something like "das Nutellaglas" ("the jar of Nutella"), i.e. building a compound word so that the other part of the word imposes its gender.
A well-known example is "die/das Tram" (rather a Helvetism; this words means the same as in English; the more usual German word is "die Straßenbahn). In Standard German, "Tram" is considered as an abbreviation of "die Trambahn" - so it is female. In South Germany and Switzerland, "das Tram" is used.
Nutella is a proper noun and also a loanword, I was expecting native common noun pairs. (Btw the issue exists in French too for this word, and a few others like Wifi or Gameboy)
