In his Logical Foundation of Mathematics and Computational Complexity (2013), Pavel Pudlak invites the readers to ponder about fictitious people whose natural numbers are nonstandard. His exposition is included in Section 6.1, under the subsection Interlude - Life in an Inconsistent World.
He first (implicitly) assumes the Peano Arithmetic $\mathrm{PA}$ is consistent. The theory $\mathrm{PA + \neg Con(PA)}$ is consistent by the Second Incompleteness Theorem, thus having a model $M$. He then urges us to think about a world $\mathcal W$ where the natural numbers are $M$.
He explains what kind of unnerving phenomenon occurs in $\mathcal W$.
[...] Suppose that these people discover one of the proofs of contradiction in $\mathrm{PA}$. Then they would be very frustrated when trying to determine the theory of the natural numbers. On the one hand they would see that the axioms of Peano Arithmetic are satisfied in their natural numbers, on the other hand they would know that the axioms are inconsistent. Since the axioms are true, but one can still derive a contradiction from them, they would conclude that logic fails. [...]
The problem is that I don't quite understand the passage. In particular, it is unclear what logical system the people in $\mathcal W$ use in writing "the proofs of contradiction $\mathrm{PA}$."
I'd be grateful if you could explain the passage more technically and more in detail.
To talk about these things semantically, it is easier to work in the system $\mathsf{ACA}_0$ of second-order arithmetic. This system is a conservative extension of Peano arithmetic for sentences in the language of Peano arithmetic, but $\mathsf{ACA}_0$ is able to deal directly with satisfaction (truth) predicates. If you don't know the details, for the rest of this post you can just treat $\mathsf{ACA}_0$ as a second-order version of Peano arithmetic.
A key point about $\mathsf{ACA}_0$ is that it can be axiomatized with a finite set of axioms. So we do not need to worry about "nonstandard" axioms when we look at nonstandard models: we can just assume that the finite set of axioms is used. This is not true of Peano arithmetic, which complicates Pudlak's argument - Peano arithmetic is not finitely axiomatizable. The fact that $\mathsf{ACA}_0$ is finitely axiomatizable is a good reason to look at it instead.
Suppose $M$ is a model of $\mathsf{ACA}_0 + \lnot \text{Con}(\mathsf{ACA}_0)$. This means that, in $M$, there is a natural number $c$ that codes a proof of $\lnot \text{Con}(\mathsf{ACA}_0)$. The proof coded by $c$ uses normal first-order logic, using just the axioms from $\mathsf{ACA}_0$. Because we can use a deductive system for first-order logic that only has a finite number of deduction rules, and because $\mathsf{ACA}_0$ really is consistent, $c$ must code a proof of nonstandard length when viewed from outside $M$.
Following Pudlak, let's assume that someone living in $M$ recognizes that all of the (finite number of) axioms of $\mathsf{ACA}_0$ are true in $M$, but they also recognize that $c$ codes a proof of $0=1$ from these axioms. Why is this not a contradiction?
For the person in $M$ to see the contradiction, they would need to prove by induction that, for each coded proof and every $n$, if all the statements on lines $0, 1, \ldots, n$ of a proof are true, then so is the statement on line $n+1$ (assuming the proof has $n+1$ or more lines). If they could prove that, they would be able to prove that $0=1$ is true in $M$, even though they know $0=1$ is not true in $M$, because $M$ satisfies $\mathsf{ACA}_0$.
The problem for the person in $M$ is that the induction principle needed in that proof is part of the $\Sigma^1_1$ induction scheme, and that scheme is not provable from $\mathsf{ACA}_0$. In fact, $\mathsf{ACA}_0$ plus the $\Sigma^1_1$ induction scheme proves $\text{Con}(\mathsf{ACA}_0)$. So the person in $M$ will see that $\Sigma^1_1$ induction fails.
That could be interpreted as "logic fails" if the person in $M$ thinks that $\Sigma^1_1$ induction is part of logic. Put more sharply, the person in $M$ would certainly think that "first-order logic is not sound" in the sense that a false sentence may be derived from true sentences in a "finite" (in $M$) number of steps. (At the same time, we know that $\mathsf{ACA}_0$ proves the soundness theorem for first-order logic - but that refers to something else, in this context.)