Here, you must use the exact same x and y values that you used in your plot command: stimsAt10Hz_outdet(:,1),AQS(:,2). You are passing in more. Polyfit does not know how to handle the extra data.
Polyfit also only returns the coefficients. Use polyval to calculate your fit's y values from a provided x vector. Then use hold on and plot commands to add your fit lines to your figure. See this example.