In general, it is not true that intersections of free submodules of a free module are free, see here. What if our ring is particularly nice?
Over $k[x_1, x_2]$, the intersection of free submodules $F_1, F_2 \subseteq F$ of a free module can be written as the pull-back $F_1 \times_F F_2$, which is free by the syzygy theorem.
What about more general polynomial rings? Are intersections of free submodules of a free modules free for $k[x_1,\dotsc,x_n]$-modules, or other Noetherian rings?