how is it possible that in Block B it has the same transaction twice? I would have thought this was something that violated validation rules

That’s exactly what the fix for CVE-2012-2459 addressed. After Bitcoin 0.6.1, core rejects blocks with duplicate txs.

commit for the fix in Core

https://github.com/bitcoin/bitcoin/commit/be8651dde7b59e50e8c443da71c706667803d06d