Have seen a number of report from others about the same thing happening, also with ProConnect Tax, but this doesn't seem to be complaints on other forums from users of other companies' tax programs.  Not sure if these are isolated problems with Intuit's systems.  You may like to call Intuit Support in the first instance to have them look into these returns.  Otherwise, respond to the notice with a copy of the return they requested along with the e-file confirmation as proof of filing.

From a February 19 letter to the Commissioner, by the chairman of the House Ways and Means Committee:

Yesterday, we learned that the IRS sent approximately 260,000 CP59 notices to
taxpayers who the IRS claimed did not file a 2019 tax return. The IRS continues to have
a staggering backlog of unprocessed 2019 tax returns that, most recently, was reported to
include nearly 7 million unprocessed individual tax returns. In light of these severe
processing delays, it is very likely that many taxpayers receiving CP59 notices already
filed the returns that the IRS claims are outstanding. For taxpayers who have dutifully
complied with their filing obligations, these notices impose unnecessary stress and sow
confusion. For IRS employees, these notices create unnecessary work while they
struggle to meet the current demand.

https://waysandmeans.house.gov/sites/democrats.waysandmeans.house.gov/files/documents/2021.02.19%20R... 

IRS admitted they sent about 260K of these incorrectly.

https://www.irs.gov/newsroom/irs-statement-about-cp59-notices