This issue is usually caused by a converted pledge exceeding 150 installments. CRM has a hard coded limit of 150 installments for pledges.
1) Open the pledge's revenue record.
2) Click on the "Installment/Write-Off Activity" tab.
3) Review the number of installments. Pledges exceeding 150 installments will need to be addressed to apply payments.
Common methods of addressing pledges exceeding 150 installments are splitting the pledge into multiple pledges that will satisfy the 150 installment limit or, if possible, working out a new installment plan with the constituent that reduces the number of payments. (IE: switching from $15 bi-weekly to $30 monthly to reduce the installment number by half)