What this person might be experiencing is possibly something to do with the
Dunning-Kruger effect, only in reverse.
Many of those I observe in the flying world who are brimming with confidence, seem to have all the answers and just leap into aircraft and go are not necessarily the most competent, often by a long way.
Those who understand the dangers, are aware of what can go wrong and also understand the limitations of their own skills often seem slightly under-confident until they learn to mask this with a bit of bravado but underneath they are still (rightly) apprehensive.
Aviation is not natural and the best state to successfully engage with it is heightened awareness, somewhere on the line between fear and complacency.
The person in question has passed all their exams and checks and their instructor (and the CAA) has deemed them worthy to hold a licence. It could be that they know there is so much more to know (getting Rumsfeldian here) and it's preying on their mind. Best to reassure them that some of the real 'aces' have similar doubts every time they take to the air...