The software glitch is the latest of a series of problems to beset the hi-tech fleet, which have also included toilets being locked shut and passengers unable to access their cabins.
Insiders have observed that the introduction of the new trains three years ago saw the Sleeper fleet going from being the oldest and least technically advanced on the British network, with 40-year-old carriages, to becoming the most sophisticated.
It is understood the complexity of the new carriages has led to problems being caused by staff "pressing the wrong buttons”.
The latest setback comes after teething troubles such as the wrong type of bleach damaging pipes and leaving basins, toilets and showers unusable, and emergency brakes being accidentally triggered, damaging wheels.
Emergency exit windows have been locked shut because of a “circuit fault”, while passengers have also had to contend with alarms going off when carriages are coupled and uncoupled for different destinations, poor cabin cleaning which led to the contractor being sacked, and multiple locomotive breakdowns.
The Rail, Maritime and Transport union said such problems had taken their toll on Sleeper staff, and called for the service to be re-nationalised like ScotRail.
Scotland organiser Mick Hogg said: “For far too long, these new trains have been riddled with continuous faults, virtually since their introduction.
"This has led to dispute after dispute, where staff were being blamed by passengers for faults, which led to stress, anxiety, including fatigue for many.
"The key to the issue was simple - get the faults fixed so we can run a service that is fit for purpose.”
Serco said a “technical issue” with a train at its Wembley depot in London on Tuesday had meant there were fewer coaches than normal available for the “Lowlander” service to Edinburgh and Glasgow that night.
As a result, it ran without an Edinburgh portion, which would have split off at Carstairs, and the train went to Glasgow only instead.
Magnus Conn, operations director at Serco Caledonian Sleeper, said: “The issue related to a planned update to the on board train computer management system (TCMS), which rendered the train temporarily unsuitable for traffic.
"This has now been resolved, and the affected coaches are now back in operation.
“The TCMS issue on Tuesday was something we hadn’t experienced before, and we therefore removed the two affected vehicles from service in order to investigate fully.
"To minimise disruption to our guests we took the decision to merge the two Lowlander trains to run to Glasgow.
“We’re sorry for the inconvenience to our guests affected on these services.
"We provided a ticket acceptance agreement with other operators to allow all our guests to connect to their final destinations in Edinburgh.”