I applied using the app. At thd very end (after answering the questions yes or no on criminal record and prior expulsion etc etc) i was expecting the payment page. The app jumped straight to the pending page without letting me pay. I did have an application number from this though.
i started a new application and immediately was stopped as an application with this passport has already been made.
After panic i then went to the web site and checked my application using the number given. This gave me the same pending page as the app, still no payment.
after a few attempts to get to the payment page finally on the app the payment page appeared. This was about after 3 hours expired. I was then able to pay and all ok. I then completed my wifes app with no problem.
my suggestion is to keep reloading the app page to check status.
if you have questions write back.