Hi Nagu,
have you checked table DFKKINVDOC_S with the billing document number you expected to be invoiced? If the billing document number is not contained therein, then the invoicing document could be already archived.
Are you using preliminary invoicing?
Please check if table DFKKINV_TRIG contains invoicing triggers with SRCDOCCAT = PRLIN and maybe the questionable billing documents were picked up by one of the preliminary invoices? In that case, you'd have to release the preliminary invoice (e.g. via FKKINVDOC_DISP or FKKINV_CFC_MON). It's comparable to an SD-bill which is blocked for GL transfer.
If none of the above cases apply, then please collect some example in your system (billing document numbers) having this issue and create an OSS message. We need to analyse this issue in your system then. Please put a reference to this SCN thread in the OSS message as well.
Best Regards,
Georg
P.S.: Regarding the selection settings: I'm referring to the invoicing process customizing (view-cluster VC_TFK2602 -> Selection Control and node below: Enhanced Selection). In your case, I'd rule out that option as potential root cause, since the invoicing trigger was deleted by the system.