I have a random cloud generator code that puts an extra line that I cant get rid of?

This code works perfectly

The code doesn't work perfectly as posted: turtle module isn't imported; size isn't defined; the window closes immediately after drawing. Adding back missing bits, I don't get the problematic extra line you describe. (Though most likely a penup() / pendown() issue.)

I've rewritten the code below to run. And I've simplified it by using object-oriented turtle instead of the functional turtle API, made use of turtle vectors and switched the mix of radians and degrees to all radians instead:

from math import sin, cos, pi
from random import randint, uniform
from turtle import Screen, Turtle, Vec2D

N = 50  # number of points on each ellipse

# point is the center of ellipse, a is radius on x-axis, b is radius on y-axis
# ts is the starting angle of the ellipse, te is the ending angle of the ellipse
# P is the list of coordinates of the points on the ellipse
def ellipse(origin, a, b, ts, te):
    t = ts
    positions = []
    increment = (te - ts) / (N - 1)

    for _ in range(N):
        position = Vec2D(a * cos(t), b * sin(t))
        positions.append(position + origin)
        t += increment

    return positions

# draws an arc from p1 to p2 with extent
def draw_arc(p1, p2, extent):
    turtle.penup()
    turtle.goto(p1)

    a = turtle.towards(p2)
    b = pi*2 - extent
    c = (pi - b) / 2
    d = a - c
    heading = d - pi/2
    radius = turtle.distance(p2) / 2 / sin(b / 2)

    turtle.setheading(heading)
    turtle.pendown()
    turtle.circle(radius, extent, 100)

    # return the landing position of the circle
    # this position should be extremely close to p2 but may not be exactly the same
    # return this for continuous drawing to the next point
    return turtle.position()

def cloud(P):
    step = N//10  # draw about 10 arcs on top and bottom part of cloud
    a = 0  # a is index of first point
    b = a + randint(step//2, step*2)  # b is index of second point
    p1 = P[a]  # p1 is the position of the first point
    p2 = P[b]  # p2 is the position of the second point
    p3 = draw_arc(p1, p2, uniform(1.25, pi)) # draws the arc with random extent

    turtle.fillcolor('white')
    turtle.begin_fill()

    while b < len(P) - 1:
        p1 = p3 # start from the end of the last arc

        if b < len(P) / 2: # first half is top, more ragged
            ext = uniform(1.25, pi)
            b += randint(step//2, step*2)
        else: # second half is bottom, more smooth
            ext = uniform(0.05, 1.25)
            b += randint(step, step*2)

        b = min(b, len(P) - 1) # make sure to not skip past the last point
        p2 = P[b] # second point
        p3 = draw_arc(p1, p2, ext) # draws an arc and return the end position

    turtle.end_fill()

screen = Screen()

turtle = Turtle()
turtle.hideturtle()
turtle.speed('fastest')
turtle.radians()
turtle.pensize(2)

origin = Vec2D(0, 200)
size = 10
points = [] # starting from empty list

points += ellipse(origin, size*15, size*10, 0, pi) # taller top half
points += ellipse(origin, size*15, size*2.5, pi, pi*2) # shorter bottom half

cloud(points)

screen.exitonclick()