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Undeposited funds can show a negative value on the balance sheet if a payment is deposited with a date that pre-dates the payment. If a balance sheet is run between those two dates it will show a negative, reflecting the deposit withdrawing the funds but not the payment putting them in there in the first place.
If you are intentionally dating deposits before payments, then the report is reflecting the amount correctly. If this is not your normal practice, then you will want to review the payment and deposit to make sure they have the correct dates.