There are many different reasons as to why some critics may have believed that it was Percy Shelley who wrote the Preface to Frankenstein (instead of Mary Shelley). In the first Preface (1818), the text omitted much of the information provided in the later (1831).
Curiously, the name which appears at the end of the 1818 version has the name Marlow. Marlow was not a member of the party, whereas Lord Byron, John Polodori, and the Shelleys were. It was during a weather forced shut-in that the task of writing a ghost story came about.
In the 1831 Preface, Mary Shelley names her husband and refers to "his early life"--a reference that Percy did not write it. That said, some could argue that he wrote the Preface as his wife. Knowing the negativity about female writers, Percy could have been trying to prevent any negative criticism of his wife's writing ability.
Essentially, some critics may have believed that Percy wrote the tale because of its horrific nature. Many, at the time, probably thought that a Creature could only have been created by a male.
One last note worth mentioning is the fact that Mary, herself, defines her husband as the author of the tale (in the 1831 Preface). Given that she designates him as the author, it is only reasonable that some critics believe her words to be true.