1. Individual variation – Within a species there are tall ones, short ones, robust, gracile, long-waisted, barrel-chested, strong-jawed and various skin colors, all ignoring gender differences and we’re just talking about humans here. As demonstrated earlier with two species of Rhamphorhynchus, as taxa become closer and closer in genetic proximity, the influence of individual variation becomes relatively greater. And that’s entirely natural.
2. Bad data – In fossil research, ancient or cartoonish drawings may be the only data. More rarely bones are mislabeled.
3. Incomplete data – Often in fossil research the specimen is incomplete. Crushing can sometimes be just as difficult because researchers find it difficult to identify individual bones. Here’s where DGS, the digital graphic segregation technique that first colorizes photographs of the bones in crushed skeletons, which enables the operator to digitally restore them to their original positions. This similar to CT scanning techniques which do the same thing but automatically and in three dimensions seeing beneath the matrix.
4. Lack of pertinent characters in the character list – If the character list cannot differentiate an unresolved clade, then more characters are needed to recover resolution.
5. Combinations of the above – The current large reptile tree cannot resolve the exact position of SMNS 12352, which is known from a partial rostrum only. Sister taxa are also incompletely known. Perhaps more characters could resolve this dilemma. Certainly more complete specimens would help.
We all struggle with the mad scramble for more data. In Science it’s okay to work with scraps if that’s all you have, then build upon that as more data comes in.