Phase Angle between two signals

Question

I'm working on a project where I calculate the phase angle between two signals. But to keep the math/code simple I'm using simple sine/cosine function to generate the signal.

My method is as follows -

1. Generate Sine/Cosine signals

2. Select a sample size of the signal (to specify specific 'snap-shots' of the signal to be analysed)

3. Apply Hanning Window (since signal is non-periodic in my application)

4. Buffer the signal with 10 sample overlap (to do rolling FFT)

5. Take FFT of both buffered signals

6. Take the average of the FFT

7. Now extract the phase of the harmonic with the largest amplitude

8. Take the difference between the two phases.

Now, In my case since I have sine and cosine, shouldn't I get 90° as my phase difference?

I instead get either 0,-180,180 for each sample.

Thanks for your help!!

Here's my Code -

Fs=100;

x=0:0.1:32;
ISin=sin(x);
ICos=cos(x);

s = length(ISin);

samplesize=16;

Displacement=zeros(samplesize,1);
Input=zeros(samplesize,1);
n=1;
p=1;
j=1;
for i=1:s

    Displacement(j,1)=ICos(i);
    Input(j,1)=ISin(i);

    if n==samplesize

        NFFT = 2^nextpow2(samplesize); % Next power of 2 

        %% Create Hanning Window and Buffer the Data
        window=hann(NFFT);

        Displacement_Buffered=buffer(Displacement,NFFT,10);
        Input_Buffered=buffer(Input,NFFT,10);

        Displacement_Buffered=Displacement_Buffered'*diag(window);
        Input_Buffered=Input_Buffered'*diag(window);

        %% Calculate the FFT of the Signals now

        Displacement_FFT=fft(Displacement_Buffered,NFFT)/samplesize;
        Input_FFT=fft(Input_Buffered,NFFT)/samplesize;

        %Calculate the length of the frequency axis to be displayed
        f = Fs/2*linspace(0,1,NFFT/2+1);

        %Take the average
        Displacement_FFT=mean(Displacement_FFT);
        Input_FFT=mean(Input_FFT);

        %Calculate the phase angles
        Displacement_Phase=(angle(Displacement_FFT));
        Input_Phase=(angle(Input_FFT));

        %Identify the largest component

        [Displacement_Max_Value Displacement_Max_Index]=max(abs(Displacement_FFT));
        [Input_Max_Value Input_Max_Index]=max(abs(Input_FFT));

        %Get the Phase angles that correspond to the largest harmonic

        Z_Displacement=Displacement_Phase(Displacement_Max_Index);
        Z_Input=Input_Phase(Input_Max_Index);

        %Calculate the Phase angle differences

        Z_Displacement_Input=Z_Displacement-Z_Input;

        %Consolidate them in a matrix

        DispvsInput(p,1)=Z_Displacement_Input*180/pi;

        p=p+1;
        j=1;
        n=1;

    end

    %Counter
    n=n+1;
    j=j+1;
end

plot(DispvsInput)
xlabel('Sample Number')
ylabel('Phase Difference(deg)')
title('Phase Difference between Sine and Cosine')

The term 'DispvsInput' gives the phase difference between the two signals for each sample size.