Correct answer is still the first sentence. 「妹は英語をペラペラ話せる」 Most of the time, "が" can only be added after a subject I think. In the second sentence, "妹は" is already the subject of this sentence, and by putting "が" after "英語", it sounds more like "英語" itself does the action, so it sounds weird.

Correct : 妹は英語をペラペラ話してます Incorrect : 妹は英語がペラペラ話してます Second sentence doesn't make sense.