Short ballistic graphene Josephson junctions sustain superconducting current with a non-sinusoidal current-phase relation up to a critical current threshold. The current-phase relation, arising from proximitized superconductivity, is gate-voltage tunable and exhibits peculiar skewness observed in high quality graphene superconductors heterostructures with clean interfaces. These properties make graphene Josephson junctions promising sensitive quantum probes of microscopic fluctuations underlying transport in two-dimensions. We show that the power spectrum of the critical current fluctuations has a characteristic $1/f$ dependence on frequency, $f$, probing two points and higher correlations of carrier density fluctuations of the graphene channel induced by carrier traps in the nearby substrate. Tunability with the Fermi level, close to and far from the charge neutrality point, and temperature dependence of the noise amplitude are clear fingerprints of the underlying material-inherent processes. Our results suggest a roadmap for the analysis of decoherence sources in the implementation of coherent devices by hybrid nanostructures.
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