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So it looks like MATLAB is applying the filter to the "negative" and "positive" frequencies separately and I end up with two band pass regions with a null around zero. I want the whole spectrum filtered once.

[b,a] = butter(2,[.18 .3739],'bandpass');
hm = filter(b,a,Y);
figure;
plot(20*log10(abs((fftshift(fft(hm))))))

Any ideas?

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Your filter has a real-valued impulse response, which means it has a two-sided spectrum. Your filter is only applied once, but that application changes both positive and negative frequencies: -0.3739 to -0.18 and from 0.18 to 0.3729 (modulo the transition region of the filter). If the filter did not do this, you would have a low pass filter and not a bandpass filter.

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