Amniota is a tetrapod clade that includes extant mammals and reptiles, including birds, as well as a wealth of extinct taxa extending over 318 million years of Earth’s history. For over three decades, Amniota has been treated as a crown group, but the content of stem amniotes has varied among large-scale analyses of Palaeozoic tetrapods. Nine recent phylogenetic studies on Palaeozoic tetrapods, all derived from each other, have potentially changed our perspectives on amniote origins and early evolution. The first of these analyses posited that two particular clades of Palaeozoic tetrapods, Recumbirostra and Lysorophia, both previously considered to be lepospondyl stem-amniotes, are actually amniotes. This raises the possibility that early amniotes included both small fossorial and terrestrial animals, some of which show strong evidence of limb reduction. Here we show that the strange position of these small, often fossorial and limb-reduced tetrapods in Amniota is the result of two fundamental flaws: (1) the phylogenetic analysis combines two separate data matrices that were each designed to test only patterns of relationships among early anamniote tetrapods; and (2) the absence of key amniote characters. Our reanalysis of Palaeozoic tetrapod interrelationships reinstates recumbirostrans and lysorophians outside Amniota. The results of our study impact other recent studies that have simply accepted the codings in the data matrix that resulted in the hypothesis that recumbirostrans are amniotes and raises important questions about the initial diversification of amniotes and the evolution of fossoriality and limb reduction among tetrapods.