It can be an indicator of a dysplasic hip, it can also be just "one of those things."
A GP can't actually conclusively tell whether hips are dysplasic through manipulation, only the most severe cases, which actually dislocate, will be revealed through moving and checking for the click. My dd was examined by 2 different paediatricians at birth who found nothing but due to family history we got a scan.
My GP was very dismissive when I mentioned dd had been referred for an ultrasound due to family history (muttered along the lines of hips forming themselves naturally anyway). That scan revealed a dysplasic hip which dd is currently having corrective treatment for. It is much more difficult to treat once the child starts to bear weight on it.
I don't want to frighten you when you've come on here seeking reassurance and I know loads of people whose babies had odd creases and it amounted to nothing (including the physio currently treating dd). BUT if I was you I would push hard for an ultrasound so that you know for sure.
Your son, being a boy, has less chance of being affected than a girl. 70% of cases are 1st born females. The other major risk factor is being breech. Previous family history is also a factor in about a third of cases.
Chances are it's just one of those things but a scan to confirm that would put your mind at rest.