If you say "There was a call from a guy who speaks German", then you are not actually specifying what language he spoke on the phone. He may have spoken English and simply mentioned during the conversation that he is also capable of speaking German, or even that his native language is German.
It's the equivalent of "There was a call from a guy who can speak German".
If you say "There was a call from a guy who spoke German", then I would take that to mean that was the language he used on the telephone. It doesn't mean he's a native speaker, necessarily, but that's not relevant.
It's the equivalent of "There was a call from a guy who spoke German to me during the call".
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