Python lists are mutable objects and here:
plot_data = [[]] * len(positions)
you are repeating the same list len(positions)
times.
>>> plot_data = [[]] * 3
>>> plot_data
[[], [], []]
>>> plot_data[0].append(1)
>>> plot_data
[[1], [1], [1]]
>>>
Each list in your list is a reference to the same object. You modify one, you see the modification in all of them.
If you want different lists, you can do this way:
plot_data = [[] for _ in positions]
for example:
>>> pd = [[] for _ in range(3)]
>>> pd
[[], [], []]
>>> pd[0].append(1)
>>> pd
[[1], [], []]