What is wrong with my map voter script with timer and maps?

Improvements

Use :GetService() for the Workspace and Players

Use :WaitForChild() to make sure an instance exists before using it

Place newly created functions outside of your loop, this makes the code more efficient as it doesn't have to create an entirely new function each time the loop is complete and is more easily read.

For code that is repeated, you can make another local function (such as with your repeats) instead

Multiple times in your code, you call CalculateWinner() but do nothing with it, thus these calls are unnecessary

You are calling tostring() on what I presume to be a model, instead just use the Name property.

When using :FindFirstChild() make sure to check the result is not nil

Issues

spawn executes the given function in a new thread, so once the while loop in the spawned function begins, you never end it and you create multiple of these after each loop. The loop will continue during the round and end of intermission as well because of the condition. Resetting it once is enough.

Under the Touched event, you have the Line 59 "if player.Vote.Value ~= Pad then", however, the Value of "Vote" is a string, while "Pad" is an object, so this condition will always return true.

Assuming this is a ServerScript, you cannot call "game.Players.LocalPlayer", if it is a LocalScript, then the values set will not coincide for all players on the server and the below code should be placed in a ServerScript in ServerScriptService instead

Revised Server Script

-- Local Variables
local players = game:GetService("Players")

local rep = game:GetService("ReplicatedStorage")
local doneVoting = rep:WaitForChild("doneVoting")
local minutesvalue = rep:WaitForChild("Minutes")
local secondsvalue = rep:WaitForChild("Seconds")

local VotingSystem = game:GetService("Workspace"):WaitForChild("VotingSystem")
local Pad1 = VotingSystem:WaitForChild("Pad1")
local Pad2 = VotingSystem:WaitForChild("Pad2")
local Pad3 = VotingSystem:WaitForChild("Pad3")
local PV1 = Pad1:WaitForChild("Votes")
local PV2 = Pad1:WaitForChild("Votes")
local PV3 = Pad1:WaitForChild("Votes")

local VGui = VotingSystem:WaitForChild("VotingDisplay"):WaitForChild("SurfaceGui")
local PC1 = VGui:WaitForChild("Pad1"):WaitForChild("Counter")
local PC2 = VGui:WaitForChild("Pad2"):WaitForChild("Counter")
local PC3 = VGui:WaitForChild("Pad3"):WaitForChild("Counter")

local title1 = VGui:WaitForChild("Pad1"):WaitForChild("Header")
local title2 = VGui:WaitForChild("Pad2"):WaitForChild("Header")
local title3 = VGui:WaitForChild("Pad3"):WaitForChild("Header")
title1.Text = ""
title2.Text = ""
title3.Text = ""

local voteMap1 = nil
local voteMap2 = nil
local voteMap3 = nil

local minutes = 0
local seconds = 11

-- Update Status for all Players
local function UpdateStatus(text)
    for _, player in pairs(players:GetPlayers()) do
        local status = player:WaitForChild("PlayerGui"):WaitForChild("Status"):WaitForChild("Status")
        status.Text = text
    end
end

-- Vote Counter
local function UpdateDisplay()
    PC1.Text = PV1.Value
    PC2.Text = PV2.Value
    PC3.Text = PV3.Value
end

-- Picks Maps to Vote For
local function RandomizeMaps()
    local Maps = game:GetService("Lighting"):WaitForChild("Maps"):GetChildren()
    voteMap1 = Maps[math.random(1, #Maps)]
    voteMap2 = Maps[math.random(1, #Maps)]
    voteMap3 = Maps[math.random(1, #Maps)]

    if voteMap2 == voteMap1 then
        repeat
            voteMap2 = Maps[math.random(1, #Maps)]
        until voteMap2 ~= voteMap1
    end
    if voteMap3 == voteMap2 or voteMap3 == voteMap1 then
        repeat
            voteMap3 = Maps[math.random(1, #Maps)]
        until voteMap3 ~= voteMap2 and voteMap3 ~= voteMap1
    end

    title1.Text = voteMap1.Name
    title2.Text = voteMap2.Name
    title3.Text = voteMap3.Name
end

-- Determine Winning Map
local function CalculateWinner()
    local padVotes = {
        [voteMap1.Name] = PV1.Value,
        [voteMap2.Name] = PV2.Value,
        [voteMap3.Name] = PV3.Value,
    }

    local highest = 0
    local pad = nil
    for map, vote in pairs(padVotes) do
        if vote > highest then
            highest = vote
            pad = map
        end
    end

    if pad == nil then
        local padTbl = {voteMap1.Name, voteMap2.Name, voteMap3.Name}
        pad = padTbl[math.random(1, #padTbl)]
    end

    return pad
end

-- Reset Pads
local function ResetVotes()
    wait(1)
    doneVoting.Value = true
    PV1.Value = 0
    PV2.Value = 0
    PV3.Value = 0
    PC1.Text = 0
    PC2.Text = 0
    PC3.Text = 0
    title1.Text = ""
    title2.Text = ""
    title3.Text = ""
    voteMap1 = nil
    voteMap2 = nil
    voteMap3 = nil

    for _, player in pairs(players:GetPlayers()) do
        local plyrVote = player:WaitForChild("Vote")
        plyrVote.Value = "NA"
    end

    wait(5)
    doneVoting.Value = false
end

local function WaitTime(min, sec)
    minutesvalue.Value = min
    secondsvalue.Value = sec

    repeat
        if secondsvalue.Value <= 0 then
            minutesvalue.Value = minutesvalue.Value - 1
            secondsvalue.Value = 59
        else
            secondsvalue.Value = secondsvalue.Value - 1
        end
        wait(1)
    until secondsvalue.Value <= 0 and minutesvalue.Value <= 0
end

-- Give Players Voting Tags
players.PlayerAdded:Connect(function(player)
    local Vote = Instance.new("StringValue")
    Vote.Name = "Vote"
    Vote.Parent = player
    Vote.Value = "NA"
end)

-- Prepare Pads
for _, Pad in pairs(VotingSystem:GetChildren())do
    if Pad.Name ~= "VotingDisplay" then
        Pad.Touched:Connect(function(hit)
            if hit and hit.Parent and players:GetPlayerFromCharacter(hit.Parent) then
                local player = players:GetPlayerFromCharacter(hit.Parent)
                local plyrVote = player:WaitForChild("Vote")
                if plyrVote.Value ~= Pad.Name then
                    Pad:WaitForChild("Votes").Value = Pad:WaitForChild("Votes").Value + 1
                    if plyrVote.Value ~= "NA" then
                        local padToSubtract = VotingSystem:FindFirstChild(plyrVote.Value)
                        if padToSubtract then
                            padToSubtract:WaitForChild("Votes").Value = padToSubtract:WaitForChild("Votes").Value - 1
                        end
                    end
                    plyrVote.Value = Pad.Name
                    UpdateDisplay()
                end
            end
        end)
    end
end

while true do
    UpdateStatus("Intermission")
    WaitTime(0, 15)

    UpdateStatus("Voting In Progress")
    RandomizeMaps()
    WaitTime(0, 10)

    -- Declare Winning Map
    local mapWinner = CalculateWinner()
    -- Reset Pads
    ResetVotes()

    UpdateStatus("Loading Map "..mapWinner)
    wait(5)

    UpdateStatus("Round In Progress")
    WaitTime(minutes, seconds)

    UpdateStatus("Game Over!")
    wait(5)
end

Additionally, I would be placing your maps under ServerStorage or ReplicatedStorage instead of Lighting.