Before the last few lines of "Desiree's Baby," are there any clues given by the author which hint at the true cause of the baby's appearance?

Your question relates to a literary term that is called
foreshadowing, which we can define as the way in which authors give certain hints early
on in stories about what will happen later on. Often, foreshadowing is only noticable
when we have read the story for the first time, and we re-read it again and spot how the
author has brilliantly foreshadowed the surprise ending. If we consider this excellent
story, you might like to consider the way in which forshadowing occurs through the
family background of Armand and also the way he is described. Note the information we
are given about his family background:

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The wonder was, that he had not loved her before;
for he had known her since his father brought him home from Paris, a boy of eight, after
his mother died
there.

Clearly, the ending of
the story, and the note that Armand discovers from his mother, makes the convenient
absence of his mother from the story very important, especially given the concern about
the supposedly more suspect background of the unknown
Desiree.

Secondly, another major piece of foreshadowing
occurs in the way that Armand is described. He is sad to have a "dark, handsome face."
This subtle use of the word dark, compared to the whiteness of Desiree, is a descriptive
note that we go back to after finishing the story and reassess, recognising the clue
that Chopin plants in this one word concerning the origins of the darkness of Desiree's
baby.