The intrinsic uncertainty of fluid properties, including the equation-of-state, viscosity and thermal conductivity, on boundary layer stability has scarcely been addressed. When a fluid is operating in the vicinity of the Widom line (defined as the maximum of isobaric specific heat) in supercritical state, its properties exhibit highly non-ideal behavior, which is an ongoing research field leading to refined and more accurate fluid property databases. Upon crossing the Widom line, new mechanisms of flow instability emerge, feasibly leading to changes in dominating modes that yield turbulence. The present work investigates the sensitivity of three-dimensional boundary layer modal instability to these intrinsic uncertainties in fluid properties. The uncertainty, regardless of its source and the fluid regimes, gives rise to distortions of all profiles that constitute the inputs of the stability operator. The effect of these distortions on flow stability is measured by sensitivity coefficients, which are formulated with the adjoint operator and validated against linear modal stability analysis. The results are presented for carbon dioxide at a representative supercritical pressure of approximately 80 bar. The sensitivity to different inputs of the stability operator across various thermodynamic regimes shows an immense range of sensitivity amplitude. A balancing relationship between the density gradient and its perturbation leads to a quadratic effect across the Widom line, provoking significant sensitivity to distortions of the second derivative of the pressure with respect to the density,
$\partial ^2 p/\partial \rho ^2$. From an application-oriented point of view, one important question is whether the correct baseflow profiles can be meaningfully analysed by the simplified ideal-fluid model. The integrated modal disturbance growth – the N factor calculated with different partly idealised models – indicates that the answer depends strongly on the thermodynamic regime investigated.