There seems to be confusion in the literature about that exact point.
The Literature of the Sages, Part 2 describes the perakim as subdivisions of the parshiot, and notes in footnote 370 that "the editor of the printer edition did not understand that the perakim are part of the parsha..." explaining the confusion about numbering.
However, The Anthology in Jewish Literature claims in note 10, referencing the same source the above source references that Sifra was originally organized sequentially based on how the text appears in Torah and then later superimposed on that creating confusion of parshiot vs. perakim.
Yet another opinion, Halachic Sources: From the Beginning to the Ninth Century states that originally 9 perakim were divided into 80 parshiot. Today sifra consists of 14 larger sections (which I did not deal with above) that are then divided into perakim, each of which is divided into parshiot.