The item may have been in stock when it was added to the cart but while placing an order if the system detects that it is no longer in stock, then it removes it from the cart and notifies the user as shown below:
A site administrator can also view the notification under Report > Notifications to see what product was removed and for whom.
This notification may also appear due to modified category access. In other words, if the category access for a user changes between now and when the product was added to the cart, the system removes it from the cart.
To confirm, navigate to Customers > Customer Groups and click Edit for the group to which your user belongs.
The Category Access panel on the right allows you to see whether your user has access to the category to which the removed product belongs.