There wasn't even a unified diagnosis code for COVID until April 1, and that required a herculean effort and a shirking of normal coding update processes. There were various guidances for coding, but identifying diagnosis in structured data for fast analysis was a difficult ask. (I know this to be true, I've done it across the health records of millions of patients.)
I'm sure some fault lies in the administration, but my belief is that our health system is systemically unable to properly deal with widespread pandemic, especially from a newly discovered illness.
That's one of those trade-offs that have to be considered when looking at how health care in the US should be handled in the future.