According to your requirement, I have created a sample to get this working correctly.
1. First of all in TodayViewController interface, create 3 different UIButtons and give their tag values to uniquely identify them.

Here I have given tags as: 1, 2, 3 to First, Second and Third UIButton.
2. Next you need to write the code to open your Containing App from Today Extension. In TodayViewController create an @IBAction for and connect it to all three UIButtons.
@IBAction func openAppController(_ sender: UIButton)
{
    if let url = URL(string: "open://\(sender.tag)")
    {
        self.extensionContext?.open(url, completionHandler: nil)
    }
}
In the above code, tag will be added to the url scheme to identify which UIViewController needs to be opened on UIButton press. So the url will look something like: open://1
3. In the Containing App's URL Types need to make an entry for URL Scheme, i.e

As evident from the above screenshot, there is no need to make entry for each url that you want to open from your extensions. URLs having same url scheme have only a single entry.
4. When the containing app is opened from extension, you can get the handle in AppDelegate’s application(_ : url: sourceApplication: annotation: ) method. Here, you can handle which controller to open i.e.
func application(_ app: UIApplication, open url: URL, options: [UIApplicationOpenURLOptionsKey : Any] = [:]) -> Bool
{
    if url.scheme == "open"
    {
        switch url.host
        {
        case "1":
            //Open First View Controller
        case "2":
            //Open Second View Controller
        case "3":
            //Open Third View Controller
        default:
            break
        }
    }
    return true
}
url.scheme identifies the scheme of URL i.e. open and url.host identifies the host component in the URL which is currently set to the UIButton's tag value which you can use to uniquely identify which UIButton is pressed and what to de next accordingly.
For more on Today Extensions, you can refer to: https://hackernoon.com/app-extensions-and-today-extensions-widget-in-ios-10-e2d9fd9957a8
Let me know if you still face any issues regarding this.