Why does this GUI not clone properly?

Well, this is odd. I am going to ask you to read this link about debugging (as I am assuming you are currently using Online Roblox to debug which is needless unless you are debugging DataStores.)

After you have read that, I suggest to replace your current code by the code below, and check the output to see if the prints run as expected:

local lPlayer = game.Players.LocalPlayer
local handlePart = script.Parent.Handle
local inPro = script.Parent.inProgress
local ownerName = script.Parent.ownerName
local guiOffender = script.Parent.offenderGui
local guiOfficer = script.Parent.officerGui

function startOffenderG(oPlayer)
    print("function startOffenderG commenced")
    local guiOffenderCl = guiOffender:Clone()
    guiOffenderCl.Parent = oPlayer:FindFirstChild("PlayerGui")
    print("The offender gui was placed inside: " .. guiOffenderCl.Parent:GetFullName())
    wait()
    guiOffenderCl.startUpBool.Value = true
end

function startOfficerG(oPlayer)
    print("function startOfficedG commenced")
    local guiOfficerCl = guiOfficer:Clone()
    guiOfficerCl.Parent = oPlayer:FindFirstChild("PlayerGui")
    print("The offender gui was placed inside: " .. guiOfficerCl.Parent:GetFullName())
    wait()
    guiOfficerCl.startUpBool.Value = true
end

function onHit(hit)
    print("The handlePart was touched!")
    if inPro.Value == false and hit.Parent:FindFirstChild("Humanoid") and hit.Parent.Name ~= lPlayer.Name then
        print("There is currently nothing in progress, a humanoid was found and the player hit is not the player using the tool")
        local offenderPlayer = game.Players:GetPlayerFromCharacter(hit.Parent)
        inPro.Value = true
        offenderPlayer.Character.Torso.Anchored = true
        startOffenderG(offenderPlayer)
        wait()
        startOfficerG(lPlayer)
        wait()
        local guiOfficerClone = lPlayer:FindFirstChild("PlayerGui"):FindFirstChild("officerGui")
        local guiOffenderClone = offenderPlayer:FindFirstChild("PlayerGui"):FindFirstChild("offenderGui")
        guiOffenderClone.consentString.Changed:connect(function()
            print("The consentString was changed!")
            if guiOffenderClone.consentString.Value == "no" then
                print("The consentString was set to: no")
                guiOfficerClone.deniedBool.Value = true
                offenderPlayer.Character.Torso.Anchored = false
                inPro.Value = false     
            end
        end)
    end
end

function startUp()
    wait()
    print("function StartUp commenced")
    if script.Parent.Parent:IsA("Backpack") then
        ownerName.Value = script.Parent.Parent.Parent.Name
        print("Parent of script is a backpack")
    else if script.Parent.Parent:IsA("Model") then
        print("Parent of script is a model")
        ownerName.Value = script.Parent.Parent.Name
    end
end
end

print("Script is running")
script.Parent.Changed:connect(startUp)
handlePart.Touched:connect(onHit)