Can a block cipher with fixed point permutations be a good PRP? Let $E:\{0,1\}^n \times \{0,1\}^n \to \{0,1\}^n$ be a good PRP and consider blockcipher $\widetilde{E}$ defined as follows
$$\widetilde{E}(K,X) = \begin{cases}K &amp; \text{if } X=K \\ E(K,K ) &amp; \text{if } X = E^{-1}(K,K)\\ E(K,X) &amp; \text{otherwise}\end{cases}$$
Black used this to show that Matyas-Meyer-Oseas construction which is proven in the ideal-cipher-model can fail in the standard model, i.e. it will fail if we instantiate it with $\widetilde{E}$;

So $\widetilde{E}$ is the same block cipher as $E$  with one change: we now have the invariant  that $E(K, K)= K$ for all $K \in \{0, 1\}^n$. Clearly   $\widetilde{E}$
  is a good PRP since have $E$ was:  for a randomly chosen key $K, \widetilde{E}(K,\cdot)$
 is computationally indistinguishable from a random permutation.
 

Is the claim computationally indistinguishable from a random permutation true?
We can say that for a fixed key $K$, $\widetilde{E}$ we will always output $K$ if $ K = X$
The probability of getting a single point is fixed from all permutations of $k$ elements is $\frac{(k-1)!}{k!} = \dfrac{1}{k}$.
If we turn this into permutations generated by the $n$-bit block cipher. Then we have $\dfrac{1}{2^n}$. Therefore the permutations of $\widetilde{E}$ is distinguishable and $\widetilde{E}$ cannot be a good PRP.
Any missing point?
Could one provide a formal proof for this an example?
Short answer
As Maeher said, the adversary cannot recognize which points are reprogrammed or distinguish $\widetilde E$ from $E$, given oracle access to $\widetilde E$ (or $E$). This is because the adversary who detects such points can also be used to break the PRP security of $E$ by finding the key $K$.
Formal proof
It suffices to prove that no efficient algorithm can distinguish $E$ from $\widetilde E$ via oracle access. That is, we will prove that for any efficient $A$ with $q$ query to the oracle such that
$$
|\Pr_{K}[A^{E(K,\cdot)}()=1] - \Pr_K[A^{\widetilde E(K,\cdot)}() =1]|=\epsilon, \label{1}\tag{1}
$$
it holds that $\epsilon$ is negligibly small.
To measure the advantage in a different term, first note that a difference in the oracle access to $E$ and $\widetilde E$ only happens if the adversary query $(K,K)$ or $(K,X)$ for $X=E^{-1}(K,K)$ to the oracle. Otherwise, both oracles work exactly the same and there is no chance to figure out the difference. Let's say the above event by $\rm Bad$. Then it holds that
$$
\epsilon \le \Pr_K[A^{E(K,\cdot)}()=1|{\rm Bad}] \le \Pr_K[A^{E(K,\cdot)}()|{\rm Bad}].\label{2}\tag{2}
$$
Note that whether the oracle is $E$ or $\widetilde E$ doesn't make any difference. We choose $E$ here.
What is the probability of $\rm Bad$? We define a new adversary $B$ having oracle access to $E$ to find the key of PRP as follows.

Choose a random $1 \le i \le q$.
Run $A$ with the given oracle right before $i$-th query. Let the input of $i$-th query by $X$ and with probability, $1/2$ do either

output $X$, or
query $X$ to the oracle and output the answer $E(K,X)$.



Suppose that in the $i$-th query the $\rm Bad$ event occurs. If the first case of $\rm Bad$ occurs, i.e. $A$ queries $K$ to the oracle, then $B$ outputs $K$ with probability $\epsilon/2q$ by the first action (output $X$ directly).
On the other hand, if $A$ queries $E^{-1}(K,K)$, the second action outputs $E(K,E^{-1}(K,K))=K$ that also has probability $\epsilon/2q$.
Overall, the algorithm $B$ outputs $K$ with probability $\epsilon/2q$.
However, the PRP security of $E$ says that this probability is negligibly small. This implies $\epsilon$ is small as well since $q$ is polynomially bounded (given that $A$ is efficient). Thus no efficient algorithm can distinguish $E$ from $\widetilde E$ via oracle access, and since $E$ is PRP, $\widetilde E$ is a PRP as well, which is as we desired.