Problem with application

I am currently in the UK and applied before my visa expired for further leave to remain in the UK, Due to personal circumstances I also applied for the wee waiver along side my application and within a week the home office had got in touch and invited me to go to my post office and enrol my biometrics and gave me 15 days to do so, I went the first day I received it and enrolled and paid the handling fee as requested. Today I received all my documents back from them saying my application was invalid due to non payment however I was under the impression I was waivered. Was it an error on behalf of the case worker and should I send back the application with the copy of my biometrics being done ? Or have I got the wrong end of the stick entirely. I was under the impression fees was always done before biometrics was. I am concerned as I worry how this effects my visa status here.

thank you for taking the time to read .

What was your visa status before expiring and what further leave have you applied for?

I had a valid 6 month visitor visa and have applied for discretionary leave to remain.

On what basis have you applied for discretionary leave?

I am not sure if you can switch to DLR from a visitors visa, perhaps a moderator could confirm.

I know you cannot apply for any other visa category (spouse, Tier 1/2 main or dependent, etc) if you are in the UK on a visitor visa.

Why did you think that you were exempted from the fees? See also Table 3.