This use of F creates an order depdency between loop iterations. (You're modifying F on each loop iteration). I'm not entirely sure what you're trying to do here, but perhaps you want to do something more like this?
rng('default')
x = -2.5 + 5*rand([50 1]);
y = -2.5 + 5*rand([50 1]);
v = x.*exp(-x.^2-y.^2);
F = scatteredInterpolant(x,y,v);
parfor i = 1:10
% Make a copy of F
Ftmp = F;
% Modify the copy - this is fine
vnew = x.^2 + y.^2 + i;
Ftmp.Values = vnew;
out(i) = F(i, i);
end
disp(out)
