Your post states that you work in a well known' pizza place but it also refers to the shop as having 'owners'. From this, I assume that it's a franchise operation.
Franchise holders are only allowed to buy their supplies from the company which grants the franchise. (This, of course, is so that the customer will receive exactly the same product irrespective of which shop they go to).
However, franchise holders often find that they can buy cheaper products elsewhere and substitute these products for the 'official' ones (thus making bigger profits).
Obviously, this would quickly become apparent to the franchise company if the shop simply ceased buying the official products so only a certain percentage of 'fake' products are mixed in with the 'real' ones.
The franchise company has the right to check the sales figures of the shop and, obviously, these should match the purchase figures. It's for that reason that the franchise holder records the 'unofficial' sales separately (if he records them at all).
An additional advantage to the shop owner is that he will end up with a set of sales figures which he can truthfully say has been checked by the franchise company. It will be these figures which get presented to the tax man. The shopkeeper benefits twice over because he's made extra profits to start with and then he doesn't pay any tax on those profits.
I've not specifically heard of these practices taking place in pizza chains (although I've no doubt that they take place) but the quality of the coffee you get in certain branches of a well-known burger chain varies far more than should reasonably be expected. (i.e. it's evident that the franchise holders are buying cheap coffee and substituting it for the 'official' product).
Chris