Yes, a customer can dispute an ACH payment. Account holders of personal accounts have 60 days to raise a dispute, while business accounts have 2 days. If a dispute is raised the transfer in question will be refunded, and you will be charged the failed transfer fee. There is no way to contest this reversal, so you will need to resolve the situation directly with your customer.
To avoid unnecessary reversals it is important to inform your customer that when they pay an invoice via electronic funds transfer a debit will be made to their bank account with a description as detailed in this answer.