If he even got as far as being considered for a position that involved signing the Official Secrets Act then he should have undergone either an enhanced security check or enhanced developed vetting. This is not a simple background check on PNC plus recent employment but covers:
successful completion of the Baseline Personnel Security Standard
completion, by the individual, of a DV security questionnaire
a check of both spent and unspent criminal records
a check of credit and financial history with a credit reference agency
a check of Security Service (MI5) records
a full review of personal finances
a detailed interview conducted by a trained Investigating Officer
the full review of personal finances will include an assessment of an individual’s assets, liabilities, income and expenditure both on an individual basis and taking into account the joint position with a spouse or partner.
further enquiries, including interviews with referees conducted by a trained Investigating Officer
checks may extend to third parties included on the security questionnaire - parents, friends and so on.
Unfortunately it takes a really long time to complete both ESC and EDV and for the report to be sent to the relevant parties (MI5, Police, BAe etc) so it is likely that he started employment with only partial clearance (clean bill by MI5 and no PNC history) and they would still be awaiting the third party interviews, which might have shown that he was not fit for employment in that role.