Lower central subgroups of a free group and its subgroup

For a given free group $F$ of arbitrary rank (possibly infinite), and its subgroup $G$, we address the question whether a lower central subgroup of $G$ can contain a lower central subgroup of $F$. We show that the answer is no if $G$ does not normally generate $F$. The question comes from a study of Hirzebruch-type invariants from iterated $p$-covers for 3-dimensional homology cylinders.