Your list
cluster_entries = [[0]*28]
is a list of 28 identical references to the same list. You need to use instead
cluster_entries = [ [0] for i in range(28) ]
to have 28 unique lists.
Also, a more pythonic way of iterating over idx_n
is
for i, idx in enumerate(idx_n):
print i, idx
cluster_entries[ int(idx) ].append( list_from_files[i] )