Why isn't this for loop working and stopping animations?

To stop an animation, you have to stop it from the humanoid. You can't stop it from the actual animation object, as :Stop() is not a method.

if you only want to stop the animations inside the "Animations" directory, this script should work nicely:

local Animations = script.Animations:GetChildren() -- Gets the animations

function stopAnimations()
    local playing = game.Players.LocalPlayer.Character.Humanoid:GetPlayingAnimationTracks()
    for _,Anim1 in pairs(playing) do
    for _,Anim2 in pairs(Animations) do
           if Anim1.Animation == Anim2 then
            Anim1:Stop()
                break
           end
        end
    end
end

stopAnimations() -- Fires the function

You are stopping the Animation, which isn't playing. when you want to play an animation you must load it first with the LoadAnimation() function, like this:

local Animation = --Your animation here
local Humanoid = --The humanoid which will play the animation

local AnimationTrack = Humanoid:LoadAnimation(Animation)

Then you play the track using the AnimationTrack:Play() function, and if you want to stop the track you don't say Animation:Stop(), you say AnimationTrack:Stop(). By adding all tracks into an array you can stop all of them.

Here's how the code should look like:

local Humanoid = --The humanoid which will play the animation
local AnimationTracks = Humanoid:GetPlayingAnimationTracks() -- All animation tracks

local function StopTracks()
    for i = 1, #AnimationTracks do
        AnimationTracks[i]:Stop()
    end
end --> Stop All the playing tracks

StopTracks() --> Run the function