As ksdensity returns the probability density, it can be higher than one. The integral of this function, which is the total probability, will be 1.
See the following code for example,
A1 = load('trajrmsd_I_1_1_c.txt');
A1_RMSD = A1(:,2);
[f,xi] = ksdensity(A1_RMSD);
fitobj = fit(xi', f', 'linearinterp');
integralfun = @(x)(fun(x, fitobj));
integral(integralfun, 0, 2.5)
function y = fun(x, fitobj)
y = feval(fitobj, x)';
y = max(0, y);
To consider an analogous example, if you consider a rectangle with unit area, it's height can be made arbitrarily large by making the width smaller than 1 for e.g., height = 5, and width = 0.2. The area will however remain 1.