I have a signal that looks almost like a perfect square wave. When looking at its FFT, I see that the real part has components at the fundamental and third harmonic of almost equal magnitudes. When looking at the imaginary part, I see spectral components at the fundamental and the third harmonic of notably different levels.
As far as I know, the Fourier series of a square wave has $a_n = 0$, hence I was expecting to see almost no real part of the FFT. Any idea how the signal described above might have been synthesized? 