I have plenty of excess Projected Budget Room and Total Money Available. However, when trying to increase my Scouting Budget or Player Development Budget during the Preseason, it will only let me do so in small increments. For example, I attempt to raise from $4,000,000 to $5,000,000 (1987 financials), but after I hit enter it only changes to $4,013,200. I can then enter another number, and it will only increase to $4,026,400.
I had a similar problem in a previous version, but I couldn't pinpoint what was happening. In this case, I'm fairly sure I know what the issue is. The amount of each increment is the same as my Money for Free Agents (which is limited due to a hard salary cap). For some reason it must be checking the available free agent money as a quick verification of the entered increase, rather than recalculating the budget.
See Scouting Budget under Controlled Budgets in screenshots below, in this case it went from $4,118,800 to $4,132,000 (increase of $13,200).
There are several places where a hard salary cap is not handled particularly well, one in my mind at the moment is the calculation of impact on available money on the Initiate Trade screen, it basically always says my available money won't be affected even when there will be due to the other team's players having higher salaries. It still prevents any trades that would put me or the other team over the salary cap, it just doesn't report the effect on available money properly when neither team will go over the cap.