When coupled with the already violent language of the opening lines, the word "caressed" stands out as odd. We are given the image of a rape scene, in which Zeus in the guise of a swan is forcing himself upon Leda's "helpless" and "staggering" self. However, this line presents the sort of tenderness reminiscent of the artistic depictions of the myth by Da Vinci, Michelangelo, and many others, as if the scene at least has elements of seduction or mutual endearment between Leda and the swan. This mix of violence and love creates a sense of confusion for the reader as well as for Leda that is difficult to reconcile with the rest of the poem.
It is difficult to determine Yeats' intent in using this phrase, as it seems to contradict the overall brutality of the piece. In fact, the tenderness of that single word in a way heightens the brutality by way of comparison, as it is essentially the only word in the poem that does not immediately connote violence, anger, brutality, etc. The meaning of "caress" is altered to suit Yeats' purposes, which seem to be to unify these two aspects -- ugliness and beauty, tenderness and brutality, masculinity and femininity -- until they are almost indistinguishable. Indeed, any tenderness to the word is ignored or else immediately disregarded in light of its surroundings.