1. Why should 'already' not be used with the present continuous?
"Scientists say that carbon dioxide will warm the Earth, but that is already happening."
You didn't find that there was no such usage. What happened was that you didn't find an example of that usage. This is not surprising, since dictionaries are primarily books that give definitions of words, not usages.
2. They could have used the simple past "was predicted". Certainly "had been previously predicted" is wordy; they could have omitted 'previously'. But it's hard to argue the case without the complete context. "Previous" to what, for example. Another point is that although the first clause is in the present simple tense, that is the "timeless" usage of the tense. They have obviously obviously observed the particles dropping (in the past), and the predictions were made before that.
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