If that's its behaviour, it's a severe bug.
It should only use ligatures if they are defined in the font (and that is indeed what happens in my reader). So, either ADE 2.0 is broken or the font is broken (i.e. it defines a ligature that it doesn't really have). Is the font maybe a subset? In that case the subsetting software is probably breaking the font.
I don't know if you can disable ligatures in ADE, probably not (I believe the Cybook Odyssey allows that, though). You could prevent ligatures by inserting zero-width-no-break spaces (whatever the code is) between the letters... but that's an UGLY hack for this use.