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Why are South American Indigenous languages difficult for linguists to classify?

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distribution of aboriginal South American and circum-Caribbean cultural groups — South American Indian Distribution of aboriginal South American and circum-Caribbean cultural groups.

South American Indigenous languages are notoriously difficult for linguists to classify due to a combination of extreme linguistic diversity, historical factors, and methodological challenges.

Key reasons for these difficulties include:

Fragmentary Data: Many languages are extinct or poorly documented, leaving researchers with insufficient or unverifiable material. In some cases, no linguistic records exist at all, making them unclassifiable rather than simply unclassified.12
Methodological Limitations: Most classification attempts have relied on inspecting vocabulary or structural similarities without applying rigorous, standardized criteria. Techniques like glottochronology and lexicostatistics have been used, but there is little consensus on how to distinguish between dialects, languages, families, and stocks.1
Nomenclature Anarchy: There is a lack of standardized naming conventions. Names often stem from European misinterpretations, derogatory terms used by rival groups, or generic labels, leading to the same name being applied to different languages or multiple names for a single language.1
Rapid Extinction and Accessibility: The rapid loss of languages, combined with a shortage of linguists and the remote locations of many remaining groups, has severely hindered descriptive and historical research.3