Question about identical txids/merkle tree in Developer guide
It refers to a (practically impossible) edge case due to how unbalanced merkle trees work.

Let's say you manage to find two transactions with the same transaction ID, T1 and T2.

Now, let's build the merkle tree for a very simple block:

                 H(A, B)
                /       \
       A = H(CB,X)       B = H(T1,T2)
        /        \        /         \
       CB        X       T1         T2


Now, if you were to build the same merkle tree without T2, you have an unbalanced tree with only 3 leaves. To fix this, the last leaf is duplicated, as such:

                 H(A, B)
                /       \
       A = H(CB,X)       B = H(T1,T1)
        /        \        /         \
       CB        X       T1         T1


However, since T1 and T2 share a transaction hash, your merkle root actually ends up being identical to the tree with two separate transactions.

Since the merkle root is the same, the proof of work for a block containing T1 and T2 would also be valid for a block containing only T1.

Thus, if the first block is considered invalid by an honest node, when it sees a second block arrive with the same block header, it may dismiss it as invalid automatically based on the cached status on the original block's header, even though the second block does not contain T2, and is in effect a different, potentially valid, block.