Proto-languages are usually unattested, or in some cases only partially attested

Moreover, a group of languages (such as a dialect cluster) which are not considered separate languages (for whichever reasons) may also be described as descending from a unitary proto-language.

No trees but the smallest branches are ever found to be perfect, in part because languages also evolve through horizontal transfer with their neighbours. Typically, credibility is given to the hypotheses of highest compatibility. The differences in compatibility must be explained by various applications of the wave model. The level of completeness of the reconstruction achieved varies, depending on how complete the evidence is from the descendant languages and on the formulation of the characters by the linguists working on it. Not all characters are suitable for the comparative method. For example, lexical items that are loans from a different language do not reflect the phylogeny to be tested, and, if used, will detract from the compatibility. Getting the right dataset for the comparative method is a major task in historical linguistics.

The bias of the researchers regarding the accumulated implicit knowledge can also lead to erroneous assumptions and excessive generalization. Kortlandt (1993) offers several examples in where such general assumptions concerning "the nature of language" hindered research in historical linguistics. Linguists make personal judgements on how they consider "natural" for a language to change, and

"[as] a result, our reconstructions tend to have a strong bias toward the average language type known to the investigator."

Such an investigator finds themselves blinkered by their own linguistic frame of reference.

That Proto-languages remain unattested is evident. As Nicholas Kazanas puts it:

"The first fallacy is that the comparative method is “scientific” and can offer predictions."