Script doesn't work with table, works with single value?

Hello. You have to use an in pairs loop. It loops through a table. Try this:

local enabled = true
local ding = game.Workspace.Sounds.Ding             -- sound
local parts = {game.Workspace.Configuration.Koala1, game.Workspace.Configuration.Koala2, game.Workspace.Configuration.Koala3}    -- name
local player = game.Players.LocalPlayer
local mouse = player:GetMouse()
local UserInputService = game:GetService("UserInputService")
local gui = player:WaitForChild("PlayerGui")
local toolup = gui:WaitForChild("clickE")
local maxpickup = 20
local KoalaGUI = player.PlayerGui.KoalaAdd


    local pp = player.leaderstats.Credits
    UserInputService.InputBegan:Connect(function(input,gameProccesedEvent)

        local item = mouse.Target
        local distance = player:DistanceFromCharacter(item.Position)
for i, part in pairs(parts) do
    if mouse.Target == part and enabled == true and distance <= maxpickup and input.KeyCode == Enum.KeyCode.E or input.KeyCode == Enum.KeyCode.ButtonB then
            ding:Play()
            local newkoala = KoalaGUI:Clone()
            newkoala.Parent = game.Players.LocalPlayer.PlayerGui
            newkoala.Enabled = true
            part.Position = Vector3.new(100,100,100)
            enabled = false

            part.Transparency = 1
            part.CanCollide = false

            game.ReplicatedStorage.KoalaEvent:FireServer()

    wait(5)
            newkoala:Destroy()
            enabled = true
            part.Transparency = 0
            part.CanCollide = true


    end
end
    end)

Please accept and upvote this answer if it helps.