Although HW has answered your question negatively for greatest lower bounds, there is a closely related poset for which greatest lower bounds indeed exist. Instead of an individual free factor $A$, first consider its conjugacy class $[A]$. Then, instead of individual conjugacy classes of free factors $[A]$, consider a "free factor system" (in the language of Bestvina-Feighn-Handel): a finite set $\mathcal{F} = \{[A_1],\ldots,[A_k]\}$ such that there exists a free factorization of the form $F_n = A_1 * \cdots * A_k * B$ where $B$ may or may not be trivial but all the $A_i$'s are nontrivial. The partial ordering $\mathcal{F}\sqsubset \mathcal{F}'$ is defined by requiring that for each $[A] \in \mathcal{F}$ there exists $[A'] \in \mathcal{F}'$ such that $A$ is conjugate to a subgroup of $A'$. 

The Kurosh Subgroup Theorem can be translated into the statement that this poset has greatest lower bounds. The greatest lower bound of $\mathcal{F}$ and $\mathcal{F}'$ is 
$$\{[A \cap A'] \, | \, [A] \in \mathcal{F}, [A'] \in \mathcal{F}', A \cap A' \ne 1\}
$$