Pressing down and holding a key shows the following bubble in OSX for me:

This bubble is used for inputing non-english letters by selecting one of the offered choices. This works fine throughout OSX - the character created by pressing the key is replaced with the choice from the bubble. But in Atom the choice from the bubble is added to the character already there, it doesn't replace it (which is wrong):

So, pressing and holding Z gives a range of choices, and selecting one of those choices should result in a Ž letter (for example), but in Atom I get ZŽ. The same happens for all other letters I try to create using this input method.