Collections all products count discrepancies

We have noticed a discrepancy in the number of products for collection ‘All’ mentioned in /admin/collections, and the actual number of products available to end users on the /collections/all page.

We are seeing it on almost 15 stores we’ve built. In total the difference is 7058 products.

Here are screenshots from one of the stores:

Calculations 13310 - 12625 = 685

Admin:

/collections/all page:

So, the questions are - What the possible reasons? And how we can prevent this difference?