There are several causes ...but originates from the same issue.

QuickBooks handles pre-payments with a negative receivable. In other words, you received an unearned payment or deposit for a job and the sale(invoice) has not be entered or imported...

These pre-payments should be tarnsferred at the end of each month to a Liability Account normally called "Customer Deposits" or Pre-Payments ... then the entry is reversed at the beginning of the next month (if the job is scheduled to be completed within the month) to be available when the invoice is finalized.

Negatives also happen when there is an overpayment to an invoice is made, and the either the amount has not been adjusted out to Other Miscellaneous Income, or the proper refund process has not been performed.

If you are looking at a Cash Basis Balance Sheet and there is a negative A/R listed (There should be zero on a Cash Basis) it is probably due to the above ...

Almost always due to payments received but no sale to for them to be applied ...

I too can take a look and tell you for sure what is happening.