MY whole roof replaced on a chapel conversion (slates, battens,
breather) on original joists, 18 months ago - yes, mine did that too
for the first 6 months, less so now Nighttime after a very hot sunny
day would do it too.

AFAICT it's just settling, and does diminish after a few months. In
fact with mine it was like a little wave of tinkling sounds running
back and forth across the roof.

If there was visible distortion of the roof, or loud cracks like an
imminent failure of a timber, I'd worry.

Otherwise, best not to focus on it - it will only seem louder and more
intrusive because you do.

I'm also getting creaks from the 6 velux windows I put in whilst
having the roof done, or rather from the paneling around them. This
seems to be because of differential thermal movement between the
timber inside the insulation, and the joists outside.

These aren't going away, so I think I'm going to have to change the
way I've paneled in between the joists/velux on the outside and the
studwork inside, so one side has a sliding joint.