Is it permissible to dispose of the money from which the stipulated quarter for the scholarship student has not been spent, and what is the best way to dispose of it?

If the entity responsible for salaries is aware of the increase in funds, then there is no harm in taking it, especially since its repeated occurrence may indicate that there is no error or that it is tolerated. However, if the entity is unaware, then it must be informed. If it is permissible to take it, then you may dispose of it for your personal needs without reservation, whether for acts of worship like 'Umrah, or spending on parents, or Islamic projects, or other permissible things. You are not required to spend more than a quarter of it.