gpuArray does support indexing, but only limited forms are allowed within the context of arrayfun. The limitations for the GPU version of arrayfun are described in the doc.
In your case, you cannot index into A or B within iterateFunc because those are inputs to the function, rather than variables in the parent workspace.
However, in this case, arrayfun is probably not being applied at the right level. The way arrayfun is designed to work is that scalar elements of the inputs are passed to the function. So, inside iterateFunc, A and B will be scalars.
So, I suspect you need to structure your code so that either you can operate in a completely element-wise manner on A and B - and then use arrayfun, or else you fully vectorise your code so that the whole of A and B can be passed in.
