The Containment Failure emergency event says to place 2 cubes in each connected city when doing the next outbreak. If one of those connected cities already has 2 or 3 cubes, this triggers a chain reaction outbreak, add usual, but is this considered a separate outbreak? That is, should I place 1 or 2 cubes on each of those connected cities?
Pandemic co-creator Tom Lehmann gave an example (answering another question, admittedly) indicating that further outbreaks add only one cube.
In your Manila/Taipei example, each with three cubes, you will first place 2 cubes in Hong Kong, Shanghai, and Osaka; then do one chain reaction outbreak in Manilla, placing cubes in San Francisco, Sydney, Ho Chi Minh City, and Hong Kong, for a total of 10 cubes and 2 outbreaks.
This seems like a situation where the rules give some room for interpretation. I would say that any chain outbreaks should be treated as separate outbreaks, connecting cities receive 1 cube. This is how I play and we justify this by saying that a real containment failure in one city would likely only effect that city, it would have no bearing on how well other cities can contain their outbreaks.
Of course you could decide how hard you want the game to be and then decide on 1 or 2 cubes.