Consulta de soma do MySQL retornando resultado incorreto ao usar várias junções

Use os totais diretamente porque suas junções provavelmente estão criando mais linhas em combinação do que você deseja.

Tente o seguinte:

SELECT id, MAX(Total) as FinalTotal ,MAX(Payment) as FinalPayment
FROM si_invoices a 
    left join 
    (select invoice_id, sum(total) as Total from si_invoice_items group by invoice_id) b 
    on a.id = b.invoice_id
    left join
    (select ac_inv_id, sum(payment) as Payment from si_payment group by ac_inv_id) c 
    on c.ac_inv_id = a.id 
group by id

ou se o id for único:

    SELECT *
FROM si_invoices a 
    left join 
    (select invoice_id, sum(total) as Total from si_invoice_items group by invoice_id) b 
    on a.id = b.invoice_id
    left join
    (select ac_inv_id, sum(payment) as Payment from si_payment group by ac_inv_id) c 
    on c.ac_inv_id = a.id