Your indexing is incorrect, and you need another loop.
Basically you are looping over the directories, but then you try to use the directory iteration variable to indexing into the file structure. Here is the relevant part of your code:
for subfold_idx = 1 : num_subfolder
...
matContents = dir( fullfile(this_folder, '*.mat') );
... matContents(subfold_idx).name
end
For example, imagine if there are two directories, then subfold_idx will have values 1 and 2. But if there is only one .mat file in the second directory, then it will be an error to try to use subfold_idx with value 2 ! (because there is no second file).
You need to add another loop of for the files.
