Since lightlevels is a vector, and that vector might be different lengths for different files, it makes sense to store those vectors in a cell array and set one element of that cell array each time through the for loop.
[file_list,path_n] = uigetfile('.xlsx','MultiSelect','on');
if ~iscell(file_list)
file_list = {file_list}; % use { } here, by the way
end
n_files = numel(file_list);
lightlevels = cell(1,n_files); % lightlevels is a cell array now
intlist = zeros(1,n_files); % and intlist is a numeric array (in case you need it)
for i = 1:n_files
T1 = readtable([path_n file_list{i}]);
lidx = T1.Light<=4;
T1.Light(lidx) = NaN;
Tt = repmat(fix(now), size(T1,1), 1) + T1.Time;
T1.Time = datetime(Tt, 'ConvertFrom','datenum');
T1.Trigger = ones(size(T1.Time));
TT1 = table2timetable(T1);
TT1c = retime(TT1,'hourly','count');
[maxEvent,idx] = max(TT1c.Trigger);
intlist(i)=idx; % set the i-th element of intlist
hourlist = hour(T1.Time)==idx;
lightlevels{i} = T1.Light(hourlist); % set the i-th element of lightlevels
end
disp(lightlevels);
lightlevels{1}
lightlevels{2}
