In the first run of your n-loop it assignes nn 3 values. In the next run it assigns only 2 values but the 3rd value doesn't get overwritten or deleted and stays the same. You either have to clear nn or give it another index like
nn{n1,n} = F1{n1};
Maybe this code works for you:
clear
clc
close all
S = load('CCSD.mat');
F = fieldnames(S);
for n = 1:numel(F)
F1 = fieldnames(S.(F{n}));
F11{n} = F1;
for n1 = 1:numel(F1)
t = S.(F{n}).(F1{n1}).cc.t;
nn{n1,n} = F1{n1};
output{n1} = cumtrapz (t);
NF = @(p,q) max(output{n1}(t<=q)) - min(output{n1}(t>=p));
PArea{n1,n} = NF(5, 6);
end
cumulat{n} = [nn(:,n), PArea(:,n)];
end
