From the right-wing Daily Caller Trump: ‘Belgium Is A Beautiful City’ [VIDEO], we can see that he called Belgium a "beautiful city", and that it wasn't a verbal slip he immediately corrected.
So Belgium... is a beautiful city. And amazing place, magnificent buildings. I was there many many years ago. And [unaudible, he touches microphone] incredible image.
By contrast Belgium is a country:
Belgium ... officially the Kingdom of Belgium, is a sovereign state in
Western Europe bordered by France, the Netherlands, Germany,
Luxembourg, and the North Sea. It is a small, densely populated
country which covers an area of 30,528 square kilometres (11,787 sq
mi) and has a population of about 11 million people.
By size, Belgium is 136th of 195. By population, it is 77th. The metropolitan area of Brussels (the city that Daily Caller assumes Trump was referring to) has a population of 1.8 million.
As Junker doesn't seem to have been speaking in English, and translation isn't an exact process, I can't evaluate whether Junker mischaracterised Trump by talking about a village as opposed to a city.