Intuit recommends several solutions for this problem. The first solution may solve your problem, or you may need to try all of them to resolve the issue. For best results, perform the solutions in the order shown.
Choose Reports > Vendors & Payables > 1099 Summary.
Solution 1: Use the 1099 Options drop-down to show Vendors that aren't 1099 Vendors:
Solution 2: Use the 1099 Options drop-down to show Accounts that aren't 1099 Accounts:
Solution 3: Use the 1099 Options drop-down to find thresholds to set:
Solution 4: If you know there are transactions that aren't included, find the transaction and make sure they use 1099 Accounts: