To say something "calls itself" something is an informal, fairly common subtle way to express scepticism, reservation, doubt or disdain about something; particularly, the validity of its name. It's similar to prefacing "self-styled" or "so-called".
If I was to say "In English, Nerima calls itself Nerima City" in conversation, I'd be implying that Nerima might not be justified in calling itself a city, and I'd be implying that I suspected some cynical motive (e.g. self-promotion).
From the context, I'm sure this is not what the authors of this formal, factual Wikipedia article intended, I'm sure it's an accident of translation. It's possible they might have been reflecting the unusual nature of referring to a ward of Tokyo as a city in its own right, but it would be unusual for Wikipedia to do so in such a way.
It's very easy to find scores of real-life examples of this usage that are clearly expressing skepticism or doubt. Since it's generally an informal and negative phraseology, most of these I examples I found through web searches were from dubious-looking forums or agenda-pushing sites, so forgive me for not linking to them... There were also a couple of published books using this phraseology in the first few pages of results, which I have linked to.
The tiny island-State, currently verging on poverty, calls itself 'great Britain.' It takes gall... [anti-Britain rant continues]
The organization MENSA, which calls itself “the high IQ society,” requires an IQ score of 130 or higher for membership... [goes on to ask if this is really a remarkable score]
Our first visit to the cafe which calls itself 'nailsworth's quietest cafe'!! [damning 1-star review of said cafe]
A group called NARAL, which calls itself a feminist organization... [goes on to attack this organisation]
Israel, which calls itself a Jewish state... [you don't need me to tell you where this one's going...]
...activities, and weaknesses of the group that calls itself the “Islamic State” [ book critically examining whether it does resemble a functioning state ]
For somewhere that calls itself “Great” Britain, you sure don't shout about it. Why are you such negative whiners here? [as a Brit I'll admit this is a fair question... but as a pedant I'll point out that the 'Great' was introduced to distinguish the largest of the British Isles variously from other neighbouring islands such as Ireland, or from Brittany in France ]
It's not exclusively used with a negative connotation, but since it commonly is, in cases where it isn't, that's usually made explicitly clear:
Yarmouth rightly insists on calling itself 'Great' and has done so for 800 years. This was originally to distinguish the town from 'Little Yarmouth' across the river [ book about the history of the English town Great Yarmouth ]
Even here, the phraseology communicates the fact that many people might question or dispute the greatness implied by the name "Great Yarmouth" (which is not an especially large or famous town).