The CRTC sent letters to both companies this week seeking answers after it received viewer complaints about the May 20 finale on CBS.
The "Late Show with David Letterman" was due to end 20 minutes later than its usual hour-long duration, but the show ran longer than expected as Letterman was sent off by a host of guest stars including Steve Martin, Tina Fey, Bill Murray and the Foo Fighters.
At the end of the show's scheduled time slot, Rogers and Shaw viewers saw Letterman's show cut off as the channel switched from the CBS feed to other programming.
A spokesman for Rogers Communications (TSX:RCI.A) said that due to an "internal miscommunication," customers watching its CBS feed on cable TV in Ontario, New Brunswick, and Newfoundland and Labrador missed about a minute of Letterman's show before the channel returned to the feed.
"We apologize to our customers for the issue with the Letterman broadcast," said Kevin Spafford. "We're taking active steps to prevent errors from happening in the future, including the development of better processes through an industry working group."
In their complaints to the CRTC, some Shaw customers said their channels did not switch back to the CBS feed and they were denied the chance to watch Letterman's farewell.
Chethan Lakshman, a spokesman for Shaw Communications (TSX:SJR.B), said the company is committed to developing an industry-wide approach to the issue.
"We are investigating the events that led to the issues with the final broadcast of the 'Late Show with David Letterman' with the objective of preventing such errors in the future," Lakshman said in a statement. "Shaw deeply regrets this error and we apologize to our customers who were impacted."
The problem stems from simultaneous substitution, where programs broadcast from the United States are aired on Canada networks that replace American ads with Canadian ones.
The practice can lead to errors on live TV if Canadian broadcasters don't align their commercial breaks with American ones or they switch from one American feed to another before a show is finished.
In the case of the interrupted Letterman finale, some viewers unleashed their anger to the CRTC. The regulator passed on those concerns to both Rogers Communications and Shaw Communications.
The error left people missing "the final goodbye from a legend," Rogers customer Jay Loftus said.
"Thank you for allowing CTV and Global to ruin access to media, and the occasional culturally significant moment."
Customer Calvin Daling also took issue with the problem that disrupted Letterman's farewell.
"After 33 years of being on TV, can he not go an extra few minutes?" Daling said.
Simultaneous substitution has been under the microscope since the CRTC began reviewing TV regulation last year.
In January, the CRTC said the Super Bowl and the famous ads that go along with it will become free of the simultaneous substitution rules, beginning in 2017.
"With such focus put on the execution of simultaneous substitutions in the last few months, it is surprising that these errors continue to happen — particularly during such a widely-publicized television event," the CRTC said in its letters to the cable companies this week, promising "meaningful consequences" if the errors continue.
The CRTC has said broadcasters and distributors who make such mistakes repeatedly could be forced to give refunds to customers and lose the right to simultaneous substitution for a period of time.
The regulator has asked both companies to formally respond by Tuesday.
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