I had it suggest some parameters for BCFtools and it suggested parameters that would do the opposite of what I wanted to do. I pointed out the error and it apologized.
It also is not taking any initiative to check things, but wants me to check them (ie: file contents, etc.).
And it is claiming that things are "too complex" or "too difficult" when they are super easy. For instance refreshing an AWS token - somehow it couldn't figure out that you could do that in a cron task.
A really really bad downgrade. I will be using Codex more now, sadly.