This is a bug in your code, rather than in Python.

A simpler example, for the purposes of explanation:

>>> root, total = [0], []
>>> total.append(root)
>>> total  # good so far
[[0]]
>>> root[0] = 1   # modify root
>>> total  # note that total changes here!
[[1]]
>>> total.append(root)
>>> total
[[1], [1]]

In effect, total contains two references to the same list.  Modify that list, and you'll see those changes reflected in `total` as well.