I am getting my prestige points in game but they are not showing in the store. I cant buy prestige crates because of that.
On the xbox version the prestige points don't always show up immediately - but will get applied eventually. The longest I've had to wait is until I've done the next days daily challenges, upon which I'll usually get both days at once.
FIFOm - Ubi-Viral gives a couple of links in his post.
There is another option if the issue is a consistent one - and that is to capture your gameplay footage showing you completing the challenges and going into the ingame store (if you start recording about 10 seconds before you complete the final challenge then go into the store via the ingame menus, that should be plenty of evidence) - and then simply put a link to that video online here in this topic - or over on the Ubisoft Facebook or Twitter pages (links above in Ubi-Virals post) - it should provide all the evidence they need.
Thanks for the assist, gunbladelad! Much appreciated.