It didn't. When the CDC got the EUA for that test they made it clear it was to detect SARS CoV-2 only.
That's what it did and it never confused the influenza virus with the coronavirus causing Covid.
There are now approved test panels that can identify SARS CoV-2, influenza and other respiratory virus from a single sample and the CDC is recommending labs use one of those.
After December 31, 2021, CDC will withdraw the request to the U.S. Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) of the CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel, the assay first introduced in February 2020 for detection of SARS-CoV-2 only. CDC is providing this advance notice for clinical laboratories to have adequate time to select and implement one of the many FDA-authorized alternatives.
Visit the FDA website for a list of authorized COVID-19 diagnostic methods. For a summary of the performance of FDA-authorized molecular methods with an FDA reference panel, visit this page.
In preparation for this change, CDC recommends clinical laboratories and testing sites that have been using the CDC 2019-nCoV RT-PCR assay select and begin their transition to another FDA-authorized COVID-19 test. CDC encourages laboratories to consider adoption of a multiplexed method that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses. Such assays can facilitate continued testing for both influenza and SARS-CoV-2 and can save both time and resources as we head into influenza season. Laboratories and testing sites should validate and verify their selected assay within their facility before beginning clinical testing.
FDA Announces That CDC’s PCR Test FAILED Review, Will Have Emergency Use Authorization REVOKED