Most editing dialogs have an "Apply changes" button, but some (the table dialog and extension dialogs) have "Done" instead. There's no obvious reason for this inconsistency.
|mediawiki/extensions/Graph : master||ve.ui.MWGraphDialog: don't redefine actions|
|mediawiki/extensions/VisualEditor : master||Update VE core submodule to master (e9becf4d0)|
|mediawiki/extensions/VisualEditor : master||Make extension dialog done action messages match other dialogs|
|VisualEditor/VisualEditor : master||Make table dialog done action message match other dialogs|
@Ryasmeen Is it possible you're looking at inspectors? The extension dialogs are graph, math, chem, maps, syntax highlight and pre. These and other dialogs should all have "Apply changes" - do you see those?
The inspectors still have "Done", which possibly makes more sense because with some of them the changes are applied as you make them (e.g. if you highlight a word and open the link inspector, the link styling is added straight away; when you open the math/chem/score inspectors, the formula/score updates as you type, while the inspector is still open). OTOH dialogs take over the page and any changes are only applied upon closing. (I'd be happy to discuss changing the labels on inspectors, but this task is just meant for the dialogs.)
 For math and chem, if you click on "Quick edit", it opens an inspector instead of a dialog.