It looks like you're reassigning y in your code when you call ginput. y should be the ith column of P, but it gets overwritten as the y-coordinate of your click.
Does changing the variable name work? Or, better yet, since you're never using the y value that you click, just discard it:
for i=(1:8)
y=P(:,i);
plot(time,y)
[x,~]=ginput(2);
pt1=x(1);
pt2=x(2);
peak_max(i)=max(y(pt1:pt2));
peak_min(i)=min(y(pt1:pt2));
end
