what confuses me is the difference between MUST HAVE BEEN SOMEONE
DOING and SOMEONE WHO DID
Part of your issue has to do with "someone". Someone complicates the situation. Let's use real creatures for the time being, and then you can ask more about "someone" in a separate followup question.
who likes to have personal noun or pronoun as antecedent, although sometimes people will use "who" with nameless animals and maybe even bumblebees, but that is not the general rule:
It must have been a bee that stung you.
A parent might say to a small child:
It must have been a bumblebee who stung you.
If the new shoots on the plants in the garden are gone:
A rabbit must have been nibbling on them.
It must have been a rabbit nibbling on them.
It must have been a rabbit that was nibbling on them.
A rabbit must have nibbled on them.
It must have been a rabbit that nibbled on them.
Peter Rabbit must have been nibbling on them.
It must have been Peter Rabbit who was nibbling on them.
It must have been Peter Rabbit who nibbled on them.
My car keys are gone. It must have been Jane who took them.
It must have been my sister who took them.
ODD, REQUIRING ADDITIONAL CONTEXT:
It must have been my sister who was taking them.
In order for the sentence above to be cogent, the keys must have been missing on more than one occasion.