The fossil record is incomplete. This incompleteness has many contributing factors. Geological processes may cause to confusion or error, as sedimentary deposition rates may vary, erosion may erase some strata, compression may turn possible fossils into unrecognizable junk, and various other means by which the local fossil record can be turned into the equivalent of a partially burned book, which is then unbound, pages perhaps shuffled, and from which a few pages are retrieved. Beyond geology, there remains taphonomy -- the study of how organisms come to be preserved as fossils. Here, there are further issues to be addressed. Hard parts of organisms fossilize preferentially. The conditions under which even those parts may become fossilized are fairly specialized. All this results in a heavily skewed distribution of even what parts of organisms become fossilized, and that affects which features of morphology are available for use in classification. The issue of geography enters into all this, as a consequence of the fact that living lineages occupy ecological niches, and those niches are bound to certain features of geography.
http://www.talkorigins.org/faqs/punc-eq.html