The following difficulties come in the process of identifying and classifying a new fossil –
a) Incomplete Fossil Remains – The major problem that is faced by the scientist is the unavailability of complete fossils. Due to incomplete fossils it is difficult to determine to which set of organism the fossil belong to. It is very rare to find a complete fossil.
b) Deep intensive research is required to classify the imperfectly preserved organisms from the evidence of the fossil. This research might end up in finding a new feature which was not previously discovered and thus the organism need to be re-evaluated. In case if a new species is found whose match has not been discovered yet may change the entire theory about an organism. Now a day paleontologists use better technologies to look into the DNA details of the fossils to identify its parent class.
c) There can be traits in the new species which could match with organism in various classes. In such scenario there might confusion due to conflict of identity of the new species. Further exploration is required to identify other set of characteristics which may help in deciding the final class to which the organism belong or create a new class.