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Beatrice didn't say it to state a fact, she did it to troll the hell out of him and goad him.
What I think she was referring to:
Battler was incompetent at that moment because he couldn't solve the First Twilight of Episode 2. Her criterion was "Battler is incompetent if he cannot solve the puzzle". However, once he solved the puzzle, he became competent so the Red Truth no longer applied. It did apply when she said it, because she thought he was incompetent. It is a subjective ruling, but as we have been shown the Red Truth's context must be considered.
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