Several of those dots represent things that did not happen in any MCU movie. It's possible that they represent things that happened on Agents of SHIELD but that would be unusual -- the movies have steadfastly refused to acknowledge that the TV shows exist. (Though this might be an "easter egg" type of crossover.)
The major incidents that we see happening in the movies that are likely represented on the map are:
- Northeast US: Washington DC (The Winter Soldier) and New York City (Avengers) as you mentioned.
- Southwest US: Possibly the Iron Man 3 attacks by Mandarin (e.g. on Tony Stark's house?), or the Ant Man incidents in San Francisco.
- South America: In The Incredible Hulk, Hulk trashes a bottling plant in Rio de Janiero. The dot's in the wrong place for this, but it's the closest we have.
- Eastern Europe: Sokovia from Age of Ultron
- Western Africa: Lagos, from Civil War
The remainder represent locations that have no direct correlation to anything that happened in any of the movies. There are dots over what appears to be Cairo in Egypt, somewhere along the Russia/China border, southeast China around Kunming or Guiyang, and Adelaide in Australia.
There are hints of these places in Agents of SHIELD (particularly related to the "centipede project"), but nothing mentioned in any of the movies. Most likely they are just random dots added for flavor; remember that the Avengers have been actively hunting HYDRA for years by this point, with the idea being that they are constantly going into other countries and causing problems. It stands to reason that we didn't see every one of those incidents on-screen.