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The output of the MAX7410 is typically -3dB (0.707) at its cutoff frequency and its spec's are from -2.4dB to -3.6dB.
You will break it by exceeding its max input voltage. You are feeding it a 9V square-wave and its absolute max input is its supply voltage plus a tiny amount. I recommend attenuating the input signal to a p-p amount less than its supply voltage to avoid clipping.
When you get the input attenuated to fit into the input range of the MAX7410, as Audioguru suggested, the sine wave should actually be 4/pi times the amplitude of the input square wave. If you don't understand why, Google "fourier square wave".