Yes but for argument's sake you could say the Portuguese stole took East Timor over by force from Indonesia. It never should have been seperated from Indonesia as a whole
That would be a more compelling argument if Portugal had actually occupied and taken over something that was part of an independant nation at the time. However, when the area that is now called East Timor was colonized by Portugal, it didn't belong to any nation called Indonesia, nor even to a nation that was a fore-runner of Indonesia.
When Portugal and the Netherlands colonized the island of Timor, there was at that time no connection between it and the Javanese governments that had controlled the western part of what is now called Indonesia for some time. Therefor, the forcible annexation of East Timor by Indonesia was neither historically justified, nor accepted by the Timorese in that former Portugese colony.
Perhaps some quick look into the history of an area would be wise before making claims regarding historical claims