What about all of the other objects in the world that came about through
cross-breeding, or Kil'ayim, such as the various sorts of fruits and
vegetables produced by grafting? Such items were not created during
Creation, and came into existence at a later date!
(a) YISA BERACHAH suggests that the mule is an entirely new species. It is
more novel than other forms of Kil'ayim, for all other forms of Kil'ayim at
least resemble in some way the things that they came from, whereas a mule
does not resemble a horse nor a donkey. It must have been created at
Creation.
(b) Perhaps Rashi's principle of "Ein Kol Chadash Tachas ha'Shamesh" applies
only to living creatures, and not to fruits or vegetables. Since this is the
only living creature that can be born from interspecies relations, it must
have been created during Creation. In a similar vein, perhaps Rashi is only
referring to items which are of essential use to man. Of such items, it is
only the mule that is a novel creation. (M. Kornfeld)
(c) The SEFAS EMES suggests a different understanding of Rebbi Nechemyah's
statement, other than what Rashi says. The Gemara later says that according
to Rebbi Yosi, fire and the mule were not actually created at Bein
ha'Shemashos of Erev Shabbos of Creation. Rather, at that time Hashem
"thought about" creating them, but they were only created after Shabbos,
when "Hashem endowed man with Da'as similar to His, as it were, enabling man
to have the insight to create fire and to cross-breed species to create a
mule." (These two acts -- creating fire and creating a cross-bred species --
involve original creativity. This is the meaning of "Da'as" similar to
Hashem's -- the ability to create.)
When Rebbi Nechemyah says that fire and the mule were created at Bein
ha'Shemashos, it does not mean that the actual items were created, but
rather that Hashem decided to give man the *ability* to add to the world by
taking what exists and manipulating it. It therefore refers to *all* forms
of Kil'ayim, and not specifically to mules.