What causes the 'uncertainty' when a block is still relatively new I am currently looking into bitcoin and the underlying blockchain technology for an internship. More specifically, I am trying to grasp the confirmation process. Many sources I have used for my research state that after 6 blocks, a transaction is 99.9% valid. 

My question is: where does the 0.01% uncertainty about a transaction stem from?

Many thanks in advance.
An attacker could try to mine a chain of 7 blocks that would not include that transaction. That chain would replace the one where the transaction happened and "undo" it.

However, doing this is very hard, it requires the attacker to control a significant amount of hashpower and isn't guaranteed to work 100% of the time since while the attacker is mining, the other honest miners are also mining. Satoshi ran some numbers (albeit his calculations were off) in the whitepaper, section 11.

The more blocks your transaction is buried under, the higher the certainty is. It exponentially increases with every block that confirms your transaction.