That looks like your data are just a scatter all over and you're asking polyconf to evaluate the fit and the intervals over all data points, then plotting all those results.
When you do that, it evaluates the points in the order in which they exist in the raw data vectors and draws point-to-point in that order.
You forgot to attach the data so we can't reproduce,but try
[x,ix]=sort(x);
y=y(ix);
before calling polyconf and see if doesn't work out better
