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Some comments:
-i couldn't figure out how to complete the level behind door 2.
-it isnt as clear, as maybe it should be, as to which npc's are enemies, i kept killing the objective npc's :-)

In order to complete the Training you needed to blow up the oil drum, the same applies to all other Stages. I'll probably have them flash intermittently if they are the outstanding objective to remind you. As for NPCs they are meant to get in the way. You don't need to keep them alive to complete a Stage but it will impact your ranking, which might impact the ending.