This issue can occur, if the display in webstore is not checked for the item record.
The next possible reason is , if the subsidiary given in the item record and website record are not same.
The other reason can be because of the Personalized catalog view.
If this setup is done, there may be some conditions applied to it. So check the PCV .
Lists> Accounting> Items collections
Select the corresponding item collection and check the visibilty
