For Ep.1, around the time you reach the area in front of Iceburg's manor that continues to turn red again, they will mention that enemy are running to get reinforcements. I think Nami bumps into these enemy as she takes the route around? If I remember correctly, they have a name displayed over them; just follow Nami closely rather than fighting in the semi-infinite area and you should be okay.
For Ep.2, Sogeking and Franky will also suggest plans they want to do; Franky needs to go to the kitchen to get some cola and Sogeking wants to shoot across at the bridge. You also probably need to destroy the machine that makes the door close to delay Robin being taken away. These things don't come up as specific missions but you need to complete them all. If you proceed to the boss fight too quickly you can't get them.
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