There is a bug with the "Second Wave" mission, namely the sub-mission where you have to get a certain liquid. Upon delivering that, it seems impossinle to do so - the correct answer (at least in the German version) sais "I could not find it" when it actually is right there in my hand.
Edit: Oh, and the stem bolts thing... the answers of the good captain are reversed.
Second edit: The ambassador has a similar problem.
Third edit: And the negotiations, too.
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