How Do I Make Instance Stay In Place and Go Throught Blocks?

When a part is resized, it works the same as trying to change the position of a part into another part instead of using CFrame, this causes it to move to the very top of the parts on-contact. Now, how do we solve this problem? We must continuously put the - In this case - NukeBall CFramed into a position. It seems that you want the NukeBall at position (0,0,0). So, we fix this by instead of doing NukeBall.Position = Vector3.new(0,0,0), we use CFrame which ignores collision, NukeBall.CFrame = CFrame.new(0,0,0).

Finished Code Bellow, Please toss a Plus 1 rep and accept this answer if this helps and comment any questions or problems to this answer! :

notBeenTouched = true
wait(4)
function onTouch(hit)
    HumanoidIsTrue = hit.Parent:FindFirstChild("Humanoid")
    if notBeenTouched and HumanoidIsTrue then   
    notBeenTouched = false  
    NukeBall = Instance.new("Part", Workspace)
    function onBombTouch(Hit)
    Hit:BreakJoints()
end 
    NukeBall.Touched:connect(onBombTouch)       
    NukeBall.Shape = "Ball"
    NukeBall.BrickColor = BrickColor.new("Deep orange")
    NukeBall.CanCollide = false 
    notBeenTouched = false  
    NukeBall.Anchored = true
    NukeBall.CFrame = CFrame.new(0, 0, 0) -- Changed Here
    for i = 5, 100, 5 do    
    print(i)
    NukeBall.Size = Vector3.new((i), (i) ,(i))          
    NukeBall.CFrame = CFrame.new(0,0,0)-- Changed Here Too
    wait(0.1)       
    end
    NukeBall.Transparency = 0.5
    wait(0.5)   
    NukeBall.Transparency = 1
    NukeBall:remove()
    notBeenTouched = true
    end
end

script.Parent.Touched:connect(onTouch)