There's a lot of people in this thread who seem not to be up to date with what it's like in schools at the moment. For starters, there's no such thing as an NQT anymore- it's an ECT, and they are allowed to do supply for up to 5 years before qualifying. Secondly, schools don't exactly get to pick and choose who they get sent from the supply agency in most cases- especially at the end of term, it's anyone who is willing to go!
Also, it's unlikely there will have been a class TA.
It's also basically expected that anyone who is sent out on supply is capable of basic safeguarding- such as keeping track of the students in a class.
And yes, I know it's difficult, and I do agree the school were partly at fault, especially the students having their phones on them- that isn't normal at primary.
But, as others have said, not knowing where children are is a massive risk. Last year, we had Y7s leaving the school site and truanting. It's not such a big leap that a Y6 student may do the same. Or what if they had been taken very ill in the toilets and just forgotten about?
I do think OP's sister would be better off trying to get an ECT role or a longer term supply role, where she can be better supported, but I do also think if you've passed your ITT course, you ought to be able to keep track of students in a room! As others have said, you can write names on the board, or keep a list, or run a toilet pass system AND always operate one in one out!
It makes sense to me, in an unfamiliar building, that a member of SLT would have walked her out, as well.