Indeed, somethings is wrong here. Guybrush is only supposed to say "I think she's on that ghost-ship underground." when he already found it, and Herman shouldn't mention the key or the banana picker anymore, since that puzzle is already solved at this point. Otherwise, he should tell about the key you need. Then the reminder with the banana picker would make sense.
Did you found the ship already when you choose: "I came here to rescue someone"?
In addition to this, "I told you about them borrowing my banana picker and never returning it, right?" is an inventory check missing. It really shouldn't come up when Guybrush already got the key.
The main problem in the Herman dialogs is, that currently, the script makes no difference if Herman told something to Guybrush, or if he learned about it otherwise (from memos, the cannibals or the banana picker's inscription).
I think, I'll get it sorted.