How do I fix an income script which works inconsistently?

Here is my answer:

-- Always properly indent your code!

local tycoon = script.Parent.Parent.Parent
local owner = tycoon.Owner -- StringValue for the owner's name
local income = tycoon.Income -- IntValue where income is stored
local debounce = false
local cost = 100 -- Starting price
local costAdd = 115 -- Price increase each purchase
local incomeAdd = 35 -- Income increase each purchase
local times = 4 -- Number of upgrades possible
local timeNum = 0
local ServerStorage = game:GetService("ServerStorage")
local Gui = ServerStorage.MessageGui
local players = game:GetService("Players") -- the recommended method for getting the players service

script.Parent.Touched:Connect(function(hit)
	
	if hit.Parent:FindFirstChild("Humanoid") then -- want to make sure it is a player touching
		
		local player = players:GetPlayerFromCharacter(hit.Parent)

		if player and not debounce then -- more efficient ways of checking

			if not player.PlayerGui:FindFirstChild(Gui.Name) then -- you already checked for player a couple lines ago
       			Gui:Clone().Parent = player.PlayerGui

				debounce = true
				if owner.Value ~= player.Name then
					player.PlayerGui.MessageGui.Message.Alert.Text = "You are not the owner of this tycoon!"

					wait(3) -- Wait time to be touched again
					player.PlayerGui.MessageGui:Destroy()
					debounce = false
				else -- use else/elseif statements instead of return end if you can
					if player.leaderstats.Money.Value < cost then
						local mn = cost-player.leaderstats.Money.Value
						player.PlayerGui.MessageGui.Message.Alert.Text = "Insufficient funds! You need $" ..mn.. " more!"

						wait(3) -- Wait time to be touched again
						player.PlayerGui.MessageGui:Destroy()
						debounce = false
					else
						player.leaderstats.Money.Value = player.leaderstats.Money.Value - cost
						income.Value = income.Value + incomeAdd
						cost = cost + costAdd
						timeNum = timeNum + 1
						player.PlayerGui.MessageGui.Message.Alert.Text = "Upgrade complete! Income is now $" ..income.Value.. "!"

						script.Parent.Parent.Name = "Upgrade Owner's Income - $" ..cost
						if timeNum == times then
							for i = 0.4, 1, 0.01 do
								wait()
								script.Parent.Transparency = i
								debounce = true 		
							end
							script.Parent.Parent:Destroy()
						end
						wait(3) -- Wait time to be touched again
						player.PlayerGui.MessageGui:Destroy()
						debounce = false
					end
				end
			end
		end
	end
end) --properly indenting allows you to see how many ends you need

-- I hope this helps you out!

Edit:

You should not be accessing the gui from a ServerScript. Instead you should use a remote event and fire the client. An event listener in a LocalScript can open the gui and display what you need it to. You can send arguments which allow you to tell the gui what to say. Make sure that when you :FireClient() you use player as the first argument so it knows what player to affect. I also think that this will fix your error.

Have a great day scripting!