When the new company took over the loan, they took it over subject to its terms--the same terms in the original agreement, and which you had agreed to in taking out the loan. They cannot change the terms of the loan. Therefore, the new company has to apply the payments however  the original loan required. You should therefore first check your original loan documents, payment schedule, etc., to see how the money should have been applied; if it has been misapplied and the company refuses to correct that problem, you could sue them, seeking a court order that they apply the money properly and/or seeking money damages or compensation from them. Good luck.