Anonymised GPS-based mobile phone data are increasingly used to estimate population distribution and human mobility, supporting applications across disaster response, public health, urban planning and migration research. Yet whether these data fairly represent the populations they describe, particularly outside high-income countries, remains poorly understood. We quantify coverage bias for 2,478 municipalities in Mexico by comparing population estimates from a single-platform source (Facebook) and a multi-app aggregator (Veraset) against the 2020 Mexican Population Census. We find that the magnitude and spatial distribution of coverage bias differ substantially across sources. Facebook provides higher and more evenly distributed coverage, whereas the multi-app data concentrate users in larger, wealthier and more digitally connected places. Coverage bias is also spatially structured, with neighbouring municipalities showing similar levels of over- or under-coverage. Using explainable machine learning, we show that digital access and material resources are the dominant drivers of bias for the multi-app data, while demographic and population structure dominate for Facebook. Explicitly modelling spatial dependence improves the performance of statistical models for explaining bias and reveals that an appreciable share of spatial variation remains unexplained by observed covariates. These findings show that coverage bias is source-specific and spatially dependent, and provide a foundation for adjustments that improve the representativeness of mobile phone data in unequal, data-scarce settings.

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