Inaccuracies are inherent based on a wide range of variables. In particular, the array type, as well as the inversion will affect the resistivity of any layer or body.
Interpreting data based purely on apparent resistivity isn't a good idea at all! You should always try to invert the data to produce realistic conductivity distributions.
The inaccuracies are caused by the path of the current through the Subsurface. This is why the array will affect the final result (different configurations drive current in different ways). Something unusually conductive will divert current towards the body, while resistive bodies will divertv away.
To better estimate the Subsurface resistivity, you can constrain the inversion with prior knowledge. For example, sharp high contrast boundaries, which can affect the recovered values quite significantly, can be incorporated into most inversion algorithms to (usually) enhance the accuracy of the result.
To answer your question, the inaccuracy is a product of the physics - instrumentation can only do so much before the physics kicks in.
Hope this helps! (Please correct me if/where I'm wrong too!)