Using a simple example, the ticks can be fixed like so. Referencing code from here and here.
First, the case showing overlapping labels.
f[x_] := x^2 + x^3
{min, max} = {10^-12, 10^-10};
LogLogPlot[f[x], {x, min, max}, Frame -> True,
BaseStyle -> 18, FrameLabel -> {"X", "Y"}]

Removing alternate labels.
xticks = Charting`ScaledTicks[{Log, Exp}][Log[min], Log[max]];
xticks[[All, 1]] = Exp@xticks[[All, 1]];
xticks[[All, 2]] = ReplacePart[xticks[[All, 2]],
Thread[Select[Range@Length@xticks, EvenQ] -> Spacer[{0, 0}]]];
LogLogPlot[f[x], {x, min, max}, Frame -> True,
FrameTicks -> {Automatic, {xticks, Automatic}},
BaseStyle -> 18, FrameLabel -> {"X", "Y"}]
