underpayment and mistakenly chosen occupation shortage list

Hi all,

I just went back from a biometric appointment. I filed an application weeks ago with the wrong answer to whether my job is on the list of occupation shortage list. It should be a no and I filled in a yes. This led to a underpayment of my application fee. My employer told me they left a note to the HO and I will be able to make the additional payment at the biometric appointment. However, the stuff at the biometric appointment told me that he cannot see any note. So he just took my fingerprints and scanned my passport and submitted the application.

Here's my concern:
Will my application be rejected? and what happens next?

My VISA expired a month ago. Does it mean that if my current application is rejected, I am a overstayer and cannot apply within the UK?

Many thanks. This is giving me a big headache....

can anyone help?