I posted about this, in the 2016 forum. Here is the solution that solved it for us so assuming things have not changed then give it a try:
Send email to
citizenship.support@homeoffice.gsi.gov.uk - Please note that we confirmed first that the local authority had indeed sent the update to UKVI about our ceremony, and also that UKVI had the correct status on their system. The issue was with the message between UKVI and HMPO. After emailing the above address, with clear markings that it was a JCAP application, what was wrong, and our home office reference, together with DOB and full names, it was about a week to resolve the issue. Once the caseworker confirmed that the issue was fixed, we followed up with a call to HMPO to confirm that it had come through which took another 2 or 3 days for it to update onto their computer system. Once it had, then passport arrived the following day. Such a relief as we are due to fly a day after that!
Please note the service target in 2016 was 'within 20 days' so it may still be a bit early to chase this one.
Hope it works out for you.