I'm not exactly sure what your html page and test look like. Can you please elaborate a bit more about the frames and you test? If the site is live you can simple send us your test so we can test locally what is going on.
In general TestStudio flattens all the frames into single collection, so it really doesn't matter if Frame A, contains Frame B, they will be represented as different frames, so if the frame name is not unique you can deleted and use frame index instead.
the Telerik team