"He recommended that they are separated" - is this valid?

I've seen and heard this kind of construction several times now and it always bugs me. When someone recommends something, surely the verb used in the subclause should be infinitive, so:

He recommended that they be separated.

... instead of:

He recommended that they are separated.

Is there any grammatical legitimacy to the latter expression, or is it just a kind of grammatical misunderstanding that is unfortunately coming to be used commonly?

And, could the latter expression have any possibile alternative meaning or is it just incorrect?

In that construct, the subjunctive mood should be used, which happen to be “be” for to be. No, let me say that again: the present subjunctive of the verb be at the third person of the plural is “that they be”.

The distinction between subjunctive and indicative moods, however blurred it may appear to be in Modern English, is still retained in both the spoken and written word. So, “that they are separated” is simply a mistake.

"Recommend that they are" has been occurring increasingly since 1950, but is still far less common than "Recommend that they be":

See this ngram:

http://ngrams.googlelabs.com/chart?content=recommend%20that%20they%20be,%20recommend%20that%20they%20are&year_start=1500&year_end=2008&corpus=0&smoothing=3