Operator Serco denied any link to an indefinite overtime ban imposed by the Rail, Maritime and Transport union as part of a pay dispute.
Overnight trains from both Edinburgh and Glasgow to London did not run on Monday due to “last-minute illness”, while the Glasgow service did not operate on Tuesday either.
The disruption followed passengers on a London-bound service from Aberdeen on July 26 having to be taken to Edinburgh when their train was also cancelled because of insufficient staff.
Separate disruption was caused to travellers on August 6 when a carriage on a London-Glasgow service suffered a “minor technical fault” which meant the service started instead from Watford and was terminated in Motherwell when the fault recurred.
Serco said this was to enable the affected coach “to run straight into our maintenance depot at Polmadie [on the south side of Glasgow]”.
It said the London to Glasgow and Edinburgh services were also delayed by nearly one hour on August 11 by a “locomotive issue”.
Serco told The Scotsman that extra train managers would be recruited “to improve resilience”.
Caledonian Sleeper operations director Magnus Conn said: “Along with the rest of the rail industry, we have been facing some challenges with staff shortages due to a combination of illness and the impact of self-isolation guidance.
"This has led to some instances of reduced and cancelled services in recent weeks, which is disappointing given our otherwise consistently strong reliability performance this year.
"We are very sorry for the inconvenience caused to all of our guests affected by this disruption.
"It is our priority to keep our services running throughout this challenging period, but the safety of our guests is always of utmost importance.
"We are currently recruiting for additional train managers in order to further improve the resilience of our services.”
Asked whether the shortages were related to the RMT dispute, a Serco spokesperson said they were due to the “industry-wide challenges posed by a combination of illness and the impact of self-isolation guidance”.
Sleeper trains have also been disrupted by other factors, such a police incident at Waverley Station which closed lines and had a knock-on effect on services over the August 13-15 weekend.