sorry, but can you provide a reference?
3.5 FAQ says:
When my human uses
polymorph* to take the form of
another creature, he loses any extraordinary special attacks
and qualities. Does this include his bonus feat and bonus
skill points? If so, how do I figure out which feat and skill
points are derived from his racial traits?
A human’s bonus feat and bonus skill points—like most
other racial traits—are considered extraordinary qualities, and
thus are lost when the character would lose such abilities
(including when
polymorphed). This is a good reason to keep
track of which feat is your human bonus feat, since it might
have wide-reaching effects. (For instance, if Dodge was your
bonus feat, you’d lose the benefits of any other feats that have
Dodge as a prerequisite, such as Mobility and Spring Attack.)
Keeping track of where your bonus skill points are spent is
more onerous, and likely less significant to play. If most of
your skills are maxed out (that is, their rank equals your level
+3, or half that for a cross-class skill), it’s probably easiest
simply to designate one skill as the repository for all your
bonus skill points.
For ease of play, some DMs ignore this side effect, but
doing so represents a clear benefit granted to humans. Be aware
that players of nonhuman characters may resent this “freebie.”
*The question and answer uses “polymorph” to refer
specifically to spells that rely on the polymorph or alter self
spell to adjudicate their effect (including
alter self, polymorph,
polymorph any object, and shapechange), psionic powers based
on the metamorphosis power (including metamorphosis and
greater metamorphosis
), and any other effect based on either of
these lists.
For what it's worth, I agree with you that this was a lame call, though I understand how the RAW supports it.