in this code the variable o changes on its own:

x=[[-1, 7, 3], [12, 2, -13], [14, 18, -8], [17, 4, -4]]
x1=[[-8, -10, 0], [5, 5, 10], [2, -7, 3], [9, -8, -3]]
y=[[0,0,0],[0,0,0],[0,0,0],[0,0,0]]
k=True
f=0
z=[]
d=[]
while k:
    print(k)
    o=x
    print(o)
    for i in range(len(x)):
        for n in range(len(x)):
            if i!=n:
                for g in range(3):
                    if x[i][g]>x[n][g]:
                        y[i][g]-=1
                    if x[i][g]<x[n][g]:
                        y[i][g]+=1
    for i in range(len(x)):
        for n in range(3):
            x[i][n]+=y[i][n]
    for i in range(len(z)):
        if z[i]==x and d[i]==y:
            print("")   
    print(o)
    k=False


A similar error happens when I try to append x values to a list, the list is filled with the same x value (the last one that has been appended) the number of times a x value had been appended in general.

For example:

if I had a values of x at the end of the while loop as 1, 2 and 3 and I appended them to a list the list would be [3, 3, 3] instead of [1, 2, 3]. If i wrote the list out each time a new x value is appended it would write it [1] first, then [2, 2] and then [3, 3, 3] at the end. 

I am really sorry for wasting time if this is just me being really dumb and messing something up.

This isn't a bug. After this line in your code:

   o = x

both o and x refer to the same list object. So any modification you make to that list through the name "x" (for example, x[i][n]+=y[i][n]) will be seen through the name "o" as well.

There's lots written elsewhere explaining Python's assignment semantics. I highly recommend this presentation by Ned Batchelder: https://nedbatchelder.com/text/names1.html

You can also ask further questions on the Python mailing list: https://mail.python.org/mailman/listinfo/python-list

Closing here.

Leonardo, even if this were a bug, it would be a mistake to ascribe it to IDLE.  The IDLE Shell is an alternative display window. IDLE sends your code to Python and displays values computed by Python and output by print statements.  I second Mark's suggestion to first ask questions on python-list or other forums (at least until one has substantial experience with Python).