Textbook passive high pass filter with problematic fluctuation
You are feeding a high pass filter a signal with a frequency well below the filter cutoff. In that case, the filter acts as a differentiator. Thus the output is the derivative of the input.  For a square wave, the output will be a positive maximum at the positive going transition of the square wave and a negative maximum at the negative going transition of the square wave.  That explains your output waveform. Another way of looking at it is that most of the input voltage appears across the capacitor.  Since the current through a capacitor is the derivative of the voltage, the output voltage is this current multiplied by the output resistance.