Problematic character coding methods in morphology and their effects

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A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group (2018, methodology): “The comparative anatomical observations underlying this and similar characters include both the absence of a certain feature, and variation in the shape of that feature when present (the ‘no tail; red tail; blue tail’ problem; Maddison 1993; Smith 1994; Hawkins et al. 1997; Brazeau 2011).”
A new phylogeny of ichthyosaurs (Reptilia: Diapsida) (2019, methodology): “RAxML is unable to accept polymorphic data, so these were replaced with uncertainties, which is how polymorphism is treated in TNT.”
Osteology of the Late Jurassic Portuguese sauropod dinosaur Lusotitan atalaiensis (Macronaria) and the evolutionary history of basal titanosauriforms (2013, methodology): “Although problems exist with the former method, simulation studies suggest that it is the best solution when there is no logical interpretation of a character for a given taxon (Strong & Lipscomb, 1999; Brazeau, 2011).”
A high-resolution growth series of Tyrannosaurus rex obtained from multiple lines of evidence (2020, methodology): “The characters include binary and multistate transformation series, and the coding approach of Brazeau (2011) was followed for nested but independent characters.”