The most likely cause for this is the same issue that is seen when you buy a "4TB" hard disk and it's only displays as "3.63TB" in the operating system. Even though storage vendors and Windows both use abbreviations like GB and TB, they are actually using two slightly different units of measure, the storage version being based on power of 10, and the OS being based on power of 2, so, for a storage vendor 1 GB = 1,000,000,000 bytes while for the OS 1GB = 1,073,741,824 bytes (probably more accurately abbreviated GiB for Gibibyte).
Veeam displays sizes in the same way as Windows (power of 2 so technically Mebibyte, Gibibyte, Tebibyte), while the StoreOnce console displays sizes typically used by storgae vendors, so base 10. For example, my small home StoreOnce,which only has 1TB of total capacity, currently shows 1,011GB of total and 824GB of free space in the admin console, but in Veeam it displays 941.9GB total and 767.6GB free. So where did my capacity go? Nowhere, because:
1,011 GB = 941.6 GiB
824 GB = 767.4 GiB
The small rounding errors are likely due simply to the fact that the StoreOnce web console does not display decimal and I was too lazy to query the CLI to get the exact value, but the point is, there's actually no different between these two numbers, only in how they are displayed. Note that the gap between MB/GB/TB and MiB/GiB/TiB grows wider as the size goes up. You didn't share your actual values, but for a 3TB discrepancy I'd guess your usable capacity is somewhere in the 30-35TB range, perhaps a little higher.