Fault free running is, of course, only one of the criteria for acceptance. The train must also comply with the spec in other respects, such as performance, usability and maintainability.
A product as complex as a new/re-engineered train will never be perfect at handover. The question is whether it is "good enough" to satisfy the terms of the contract. It is not normally in the interest of either the customer or the supplier for costly assets to lie idle for months while modifications are developed to correct minor issues, so usually there will be an acceptance agreement that includes reservations. The supplier will commit to delivering fixes within an agreed timescale, and/or provide financial compensation.
When a TOC is desperate to get new stock into service, such as TfW with its 769s and Northern with its 195s and 331s, it may be willing to start technician and crew training in advance of formal acceptance, and then to start passenger operation while there are still significant issues that require workarounds. If, on the other hand, a TOC is more interested in obtaining penalty payments for late delivery, it will always be able to find excuses to delay acceptance.