Unable to destroy monster after negating its effects
I activated Infinite Impermanence, then chained with Torrential Tribute; I assume that the problem comes from that both effects are in the same Chain Link. Could this be the case?


I see several problems here:


Activating Torrential Tribute as a chain to Infinite Impermanence is not a valid move (Missed Timing).

The text of Torrential Tribute specifies that you can activate it when a monster(s) is summoned (emphasis mine): 


  When a monster(s) is Summoned: Destroy all monsters on the field.


This means that to activate Torrential Tribute, the last thing that must have happened is a monster(s) being summoned. In your case, the last thing that happened in the Chain was the activation of Infinite Impermanence, so you can't chain Torrential Tribute to that (see TT's card rulings).
Let's suppose for a moment that you could have activated TT that way...:

In this scenario, the reason why Number 101 was not destroyed was indeed due to the chain, specifically the Chain resolution order. When resolving Chains, they take effect in "reverse order" as they were activated (the Chain Stack):


Chain 0: Summoning Number 101
Chain 1: Infinite Impermanence to No.101
Chain 2: Torrential Tribute activated (if it where possible move)


Resolving...:


Chain 2: All monsters on the field are destroyed. As Number 101 still has it's effects enabled he can save himself by detaching an XYZ material.
Chain 1: Number 101 effects are negated by Infinite Impermanence





Next time, to successfully (and legally) negate and destroy Number 101 you should activate TT and II in reverse order: Summon->Torrential Tribute->Infinite Impermanence so it resolves Negate->Destroy.