blockchain.info seems to source transaction money from an address not in my wallet Today, I have send a transaction with too low a fee:

https://blockchain.info/tx/84eb8a6c6562a9cfedc0e82c7fbe3355615b8154e376db0a325b4ae4f26180b2

I have retrieved the twelve word pass phrase from my wallet on blockchain.info, and calculated the private keys for the addresses in my wallet. However, the address 

1PUBmT2fzVMtNWg58K67knqoz58MmCJ8pn

is not amongst these, and it is also the only address that does not show up in my blockchain.info wallet. Therefore it I can only double-spend part of my first transaction (so to void it). What is happening here?
It is likely that the address in question is a change address. Change addresses are generated using a different key derivation path than your other addresses so you will not see it if you only generated the keys at only one derivation path.

The "normal" key derivation path (a.k.a the "external keychain") is m/44'/0'/0'/i. However keys for change addresses are typically generated on a so called "internal keychain" which has a derivation path of m/44'/0'/1'/i. It is likely that you only looked at keys on the external keychain and not the internal keychain so you did not see this address.