This question deals with how Hermione had to alter her parents' passports in order to give them new identities. But what about records of them kept in government databases? If the physical passports listed one name but a different name came up in the computer when they were checked, that surely would have raised questions.
Could she have modified her parents' names in government databases without somehow getting into a government office/facility? Nothing in the books or movies seemed to indicate that she went to that extent.
I'm basing this on the assumption that the UK kept electronic records of passport info in 1997 when HPDH took place, but couldn't find a conclusive answer on that. This post indicates that machine-readable passports came into effect in 1988 and digital passports were issued starting in 1998, so it would be reasonable to assume that the government had a database of passports issued by that time.
Related: Can magic be used to modify computer data? (If they should be merged into one question, let me know)