Francis was the founder of the Franciscans in the 13th century Clare of the Poor Clares (the female branch of the Franciscans). The two worked closely together and had a sort of spiritual friendship. Now I don't want to make wrong assumptions but they were both human, working closely together. It wouldn't be impossible for the two of them to form something more then a friendship.
There's no way that we can answer this question. There is no historical evidence for them having a physical relationship, and anything else would be an assumption.
Honestly? Should we ask this question of any male-male close working relationships throughout history? Believe it or not males and females work together every day without going at each other.