Incorrectly regarded as goofs: When Grenouille meets the perfumer, at his house/laboratory, he knows where all the substances are, although he has never been there before. He is able to do this due to his heightened sense of smell, he is able to work out where specific substances are by the scent they give off.
Factual errors: Midway through the movie a whore appears with a Pekingese dog. The Pekingese were not formally introduced into Europe until midway through the 19th Century when Britain and France "sacked" the Chinese Empire (circa 1860). The Pekingese were kept exclusively in the Chinese Imperial Palace (Forbidden City) until then and maintained by eunuchs. The movie takes place in the mid 18th Century. While it may be possible British or French royalty could have had a Pekingese (although extremely unlikely), a French harlot owning a Pekingese in the 1700's is an impossibility.