I was using Abbyy dictionary; in that, 'манипул' is genitive, 'манипула' is nominative.
I didn't take the sack idea literally, I just thought the visual explanation of it was helpful.
I had overlooked that 'с' is often used with the genitive.

I asked why 'манипул попал в мешок' cannot mean 'the manipule put him into a bag' because:-

1) In speech (in English at least), I have heard 'him' omitted, so 'манипул попал в мешок' could mean 'манипул попал его в мешок'. I was asking how, given that this omission sometimes occurs, I would know from just reading that sentence that it doesn't mean 'put him in the sack.'

2) As I could not find the same expression used in any similar context anywhere else, I assumed that it was to be taken literally, in which case, as Medved said, it makes no sense to think that it was the manipule who were put in a sack; it made sense if it was Ratslayer instead.

Hence asking how I could be sure it was 'манипул попал в мешок' not 'манипул попал его в мешок'.

Is попадать always intransitive? If so, that might explain it.