I'm confused. I thought the me- prefix was used for transitive verbs. So why does it appear in an intransitive form?
"mengerti" is a transitive verb, meaning it can have an object.
The object is not mentioned in this sentence, but it's there.
You can check the existence of the object by asking apa/siapa.
Like this :
Mereka tidak mengerti.
Mereka tidak mengerti apa ?
Mereka tidak mengerti buku fisika itu.
They do not understand.
What do they not understand ?
They do not understand that physics book.