I could not test this yet after the last patch, but on recent games I found that if my A.I. ally captures one of the Resource/building points, even without a building of his on top of it, i can´t re-capture it.

That is terrible, because in one of my games the A.I. captured one of my nearest resource sites after it was destroyes and captured by an enemy. Then, I could not get it back, unless an enemy captured it again ( and then I could send my units there again to recapture it.

Has anyone else experienced something like this?

I think that you should be able to capture ANY free (without a building on top) strategic point, and not only the ones that are not your ally´s.