You are overwriting minmax_ind every time. If you find a local max, you will overwrite it if you find another one. I hope this is what you meant, I did not test the function due to it being correct by finding the min and max of the array.
You can fix this if u add another variable just like this
function minmax_ind = min_max(y)
j = 1;
for i = 2:(length(y)-1)
if (y(i-1) > y(i)) && (y(i+1) > y(i)) % if this is true, we have found a local minimum
minmax_ind(j) = i;
j = j +1;
elseif (y(i-1) < y(i)) && (y(i+1) < y(i)) % if this is true, we have found a local maximum
minmax_ind(j) = i;
j = j +1;
end
end
end
