Yes, this is one of the potential consequences when federal budgets, which are tabled on varying dates, don't align perfectly with the estimates.
As you said, the Minister of Finance's budget allocates $15 billion for the Department of National Defence that can't be completely explained by what's presented in the budget or the supplementary estimates.
The federal budget includes $15 billion for National Defence, part of which comprises investments over several years to increase spending by the Department of National Defence. However, there's no explanation for the rest of it, at least not in the information available to the public or to my office. The information in the budget isn't consistent with the main estimates documents that you're required to approve as parliamentarians.