Many transport coefficients of the quark-gluon plasma and nuclear structure functions can be written as gauge invariant correlation functions of non-Abelian field strengths dressed with Wilson lines. We discuss the applicability of axial gauge n.A=0 to calculate them. In particular, we address issues that appear when one attempts to trivialize the Wilson lines in the correlation functions by gauge-fixing. We find it is always impossible to completely remove the gauge fields n.A in Wilson lines that extend to infinity in the n-direction by means of gauge transformations. We show how the obstruction appears in an explicit example of a perturbative calculation, and we also explain it more generally from the perspective of the path integral that defines the theory. Our results explain why the two correlators that define the heavy quark and quarkonium transport coefficients, which are seemingly equal in axial gauge, are actually different physical quantities of the quark-gluon plasma and have different values. Furthermore, our findings provide insights into the difference between two inequivalent gluon parton distribution functions.