A "systems error" is being blamed by Condor Ferries for overbooking which prompted a passenger protest.
Anger was prompted at the Poole ferry terminal after 70 passengers due to travel on the Condor Liberation were left behind on Sunday.
The new fast craft had returned to service between the UK and the Channel Islands after being cancelled on Saturday because of engineering problems.
The company pledged a "thorough investigation" into the incident.
Condor said: "Unfortunately Liberation's departure was delayed because a small number of passengers prevented other passengers from boarding the ship.
"Because of tidal restrictions in Jersey, the master had to make the difficult decision to sail before she was fully loaded.”
The protests prevented a further 69 vehicles and their passengers from boarding the ferry, the BBC reported.
The company rebooked passengers on Monday's sailings and arranged accommodation in Poole.
Fran Collins, executive director of operations, told the BBC: "Whilst we understand and share customers' enormous frustration at the situation, it was disappointing that some of them took action in this way, thereby causing further inconvenience and delay."
She added: "I'd like to sincerely apologise for the disappointment and inconvenience this will cause to those passengers who are affected.
"Our port teams have been working flat out and moved swiftly to help affected passengers revise their travel plans and to book them accommodation.
"We will also conduct a thorough investigation to find out how this systems error occurred and ensure that we improve our processes to prevent it happening again."
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