Let $\phi,\psi\in\Pi_1^0$ be independent of PA. Is the disjunction $\phi\vee\psi$ independent of PA?
The answer is no, and here is a counterexample. The proof relies on the double fixed point lemma, a generalization of the usual Goedel fixed point lemma producing two statements forming a fixed point with respect to a system, and I provide a proof below. Using it, we may produce two distinct sentences $\phi$ and $\psi$ such that
In this case, each of these statements has complexity $\Pi^0_1$. Let me argue that they are independent. First, observe that both $\phi$ and $\psi$ must be true in $\mathbb{N}$. If $\phi$ were false, then there would be a standard proof of $\phi$, having no smaller standard proof of $\psi$. In particular, $\phi$ would be a provable, false statement, contradicting $\mathbb{N}\models$PA. A symmetric argument applies to $\psi$. Second, observe that neither is provable (meaning provable in PA throughout). If $\phi$ were provable, then there would be a standard proof of $\phi$, and thus there would have to be a smaller standard proof of $\psi$, and so $\psi$ would be true, and so there would be an even smaller standard proof of $\phi$. Thus, there could be no smallest proof of $\phi$, a contradiction. And the same for $\psi$. Thus, both the sentences are true unprovable assertions, and hence independent. Finally, observe that the disjunction $\phi\vee\psi$ is provable. If both $\phi$ and $\psi$ fail in a model of PA, then that model would have proofs of both $\phi$ and $\psi$, but neither statement could have the smallest proof, for if it did, then the other statement would be true, contrary to assumption. This contradicts PA, since the smallest proof of one of them must be smaller than any proof of the other. Thus, we have independent $\Pi^0_1$ statements $\phi$ and $\psi$, such that $\phi\vee\psi$ is provable. Here is the double fixed point lemma, which I believe is due to Smullyan, connected with his double recursion theorem. I use $[\phi]$ here to denote the Goedel code of $\phi$. Double Fixed Point Lemma. Suppose that $A(x,y)$ and $B(x,y)$ are two formulas, then there are sentences $\phi$ and $\psi$ such that
Proof. Let $\text{Sub}$ be the substitution operator, the primitive recursive function such that $\text{Sub}([\eta(x,y)],n,m)=[\eta(n,m)]$. Let $\theta_1(x,y)=A(\text{Sub}(x,x,y),\text{Sub}(y,x,y))$ and $\theta_2(x,y)=B(\text{Sub}(x,x,y),\text{Sub}(y,x,y))$. Let $n=[\theta_1(x,y)]$ and $m=[\theta_2(x,y)]$. Finally, let $\phi=\theta_1(n,m)$ and $\psi=\theta_2(n,m)$. Observe that $\phi\iff \theta_1(n,m)\iff A(\text{Sub}(n,n,m),\text{Sub}(m,n,m))$ $\iff A([\theta_1(n,m)],[\theta_2(n,m)])\iff A([\phi],[\psi])$. Also observe $\psi\iff \theta_2(n,m)\iff B(\text{Sub}(n,n,m),\text{Sub}(m,n,m))$ $\iff B([\theta_1(n,m)],[\theta_2(n,m)])\iff B([\phi],[\psi])$, as desired. QED Note that we can arrange that $\phi$ and $\psi$ are distinct simply by ensuring that $\theta_1(n,m)$ and $\theta_2(n,m)$ are not syntactically the same sentence, such as by replacing $\theta_1(x,y)$ with its conjunction, but ensuring that $\theta_2(x,y)$ does not have such a form. The lemma easily generalizes to any size system and indeed, to infinite systems of fixed points. 


One can in fact prove a bit more than Joel did. For example:
In particular, we can take $\psi$ to be provable and $X$ to be the set of theorems of PA, and we get a counterexample to the question. This result is due to Per Lindström, and can be found in Chapter 7 of his beautiful and very recommended book, "Aspects of Incompleteness". The proof is an elaboration of the argument with Rosser sentences. It is a basic technical lemma used in the study of the interpretability degrees of consistent r.e. extensions of PA. (The degree of $T$ is the collection of all $T'$ that are biinterpretable with $T$.) For example, Lindström uses it to show that the degrees are dense, i.e., if $a\lt b$ then there is a $c$ with $a\lt c\lt b$. By the way, the double fixed point lemma in Joel's answer is proved in Chapter 1 of Lindström's book. The reference given there is to "Theories Incomparable with Respect to Relative Interpretability", by Richard Montague, The Journal of Symbolic Logic, Vol. 27, No. 2 (Jun., 1962), pp. 195211. As far as I can see, Smullyan does not prove this version in his "Theory of formal systems", Annals of Mathematics Studies, No. 47, Princeton University Press, Princeton, N.J. 1961. The modern presentation of Rosser sentences comes from Smullyan's book, though. The review by Kreisel in Math Reviews even called the book "the most elegant exposition of the theory of recursively enumerable (r.e.) sets in existence." 


I think Carl's answer has the same error I originally madeit doesn't address that both formulas have to be $\Pi_1^0$. The negation of a $\Pi_1^0$ formula is $\Sigma_1^0$. I think the actual answer is "yes" but several edit attempts haven't got the proof right, so I'll see if I can fix it offline instead of keeping on repeatedly editing. 


This is not actually an answer but rather a comment to Joel's answer. I am not very good in models, so here is an idea how to do without them. There is a theorem of Kreisel: if a $\Pi_1^0$ statement is provable in $T+\neg Con(T)$, then it is provable in $T$. In $PA+\neg Con(PA)$ we may prove that there exists the smallest code of a proof of $\phi$ and the smallest code of a proof of $\psi$. Denote them by $n_{\phi},n_{\psi}$. Then $\phi$ asserts that $n_{\psi}<n_{\phi}$ while $\psi$ asserts that $n_{\phi}<n_{\psi}$. Then $\phi\vee\psi$ means $n_{\phi}\neq n_{\psi}$ which is provalbe if $\phi$ and $\psi$ are syntactically different. By Kreisel, $\phi\vee\psi$ is provalbe in $PA$. (Note that the numbers $n_{\phi},n_{\psi}$ do not really exist). 

