Possible that the previous keeper gave you the V5C/2 slip from an older log book and not the most recent one. In which case the reference number from the older one won't work.

Perhaps they lost the log book and applied for a replacement log book. Then the old one turned up. They should have destroyed the old one and kept the new one.

Try phoning the DVLA. Number here: www.gov.uk/contact-the-dvla

I have just bought a 2003 plate mondeo and tried taxing it online it says my 12 digit number on my v5/2 is invalid

Could the document be a fake.