We use formulas to help us understand the "laws" that govern us and our universe. Say that suddenly, unbeknownst to us, a supercomputer was introduced to our Earth that was capable of casting a mass illusion to anything that perceives outside stimuli (humans, frogs, mosquitoes, etc...). The computer is capable to manipulating all types of brains and is even capable of learning new types of brains that evolve or are created.
The computer can create any imaginable effect and apply the illusion within a given area. For example, the computer could create a large stone that doesn't actually exist in outside reality. A human could perceive that stone, pick it up and throw it at another another person and the person would feel the pain of being struck by it.
As another example, the machine creates a bug zapper. A moth's navigational system is manipulated so that it heads toward the source. The moth is "zapped" and it feels all of the same sensations it would if it was actually electrocuted. It's brain is totally seized so that it thinks it's dead. In reality, the moth could move if it were able to break the illusion, but it cannot.
Let's assume the computer isn't actively trying to push us away from discovering it. With this level of mind control, is there any sort of test or theorem humans might create to prove the existence of a reality-warping outside force (in this case, a supercomputer)?
Edit: What method (creation of new formulae?) might someone use to try and explain a new scientific phenomenon that could upheave our understanding of physics as we know them?