Supply teaching is a tough gig. Often you're not given any real briefing about school policy and procedures and if anything goes wrong due to you not understanding how the school works you're out on your ear with no rights and a potentially damaged reputation.
As an NQT, you are supposed to be supported to develop your teaching and behaviour management skills, with a mentor to provide that support alongside reduced teaching time. The fact that this support is in place is an acknowledgement of how challenging it is in the first year post training, as well as how you shouldn't be expected to know everything and make the right decisions all the time.
When you're an NQT on supply, you're left in a position where you are not adequately qualified to do the job, you don't have any support, and you don't know the policies and procedures of the school you're in. You also don't know the layout of the school or who to go to for help. It's a recipe for disaster.
What happened while your sister was taking care of the class is a safeguarding concern, but I can totally see how it happened - she's teaching a large class of children she doesn't know, there's behavioural issues, and amidst the chaos she doesn't notice the kids haven't come back.
However, the two children being found wandering around exposes the school's own failures as well as your sister's.
My questions to the school would be:
-Why did these two children feel they could not return to the classroom after going to the toilet? (Because they obviously had no fear of any consequences for this behaviour)
-Why was behaviour in the classroom so unruly in the first place (Because the children obviously had no fear of any consequences for this behaviour)
-Why was an NQT supply teacher left in sole charge of such a challenging class?
Your sister should go back to the agency with the above points. If she wasn't supported to do her job and provided with an environment in which she could safeguard the children under her care, the responsibility for what happened needs to rest with the school. A school where a Year 6 class thinks they can get away with poor behaviour is a school that has much deeper leadership problems - also evidenced by the fact they need a supply teacher for a Y6 class in the first place.