All systems have efficiency losses.
Motors are about 85-90% efficient at converting electrical energy into kinetic energy.
Most thermodynamic engines (including internal combustion engines) do not exceed 40-50% efficiency.
No system has greater than 100% efficiency, as that would violate energy conservation.
Energy conservation is essential to modern physics and engineering. If energy conservation does not hold, a whole lot of theory that we think we know also goes out the window. The thing is, using energy conservation fits in with everything we know and it makes things work properly, for it to be wrong after finding so much else works when it is considered is unlikely. On the scale of, gravity being an illusion or atoms not existing etc. No free-energy device has been subject to scientific scrutiny and found to be producing net energy. Measurements of small energy levels can be difficulty.
Certainly, I maintain if overunity is possible it will not come from playing with magnets. It will be something really esoteric, likely involving antimatter or dark energy, as they are poorly understood unlike something like magnets that have been understood for 300 years...