Multiple mutable pointers are fine. You need to be careful to ensure you don't turn them into multiple coexisting mutable references, though.
That being said I wouldn't be surprised if there were other factors that would weigh against considering FFI calls to Fil-C safe by default (e.g., Fil-C's somewhat looser bounds on what is considered a valid pointer access).
A normal C compiler actually has to worry about a lot of extreme cases.
Imagine a function takes two pointer arguments. What if they point to the same thing? What if one points to the other and is used for a write?
The nature of the code generated varies greatly if these are possibilities…