I've captured all of the Netherlands VPs in Indonesia and there hasn't been a popup for me to annex/puppet them. Is this some sort of bug? I've reloaded the game twice with no change in behaviour. Checking the statistics it has their VPs at 0
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They might have gone Government in Exile, which prevents them from surrendering unless their faction leader starts surrendering.
Check the diplomacy screen. If their surrender bar is showing full, and hovering over it shows "Government in Exile", then your only option for annexing them is to conquer the war leader (UK). If that happens, all GiEs in that faction will become conquests for the occupiers.
Note that it can take a few reloads of the game for all of the GiEs to fully surrender.