Could this also be "He is writing to them" or "on top of them" ? Is there any context or grammar that indicates which meaning is being used?
It can be "on top of them" but you understand from the context.
He is writing to them - הוא כותב אליהם. with an Alef
When the English translation says he writes on them, the meaning I get is he is literally writing on their body like with a marker. That is not correct.