What kind of thing is bad enough that it warrants multiple discussions without the junior engineer getting the hint that it’s a bad idea?

A junior engineer can make an API that can basically live forever as tech debt.

(Especially if it's an "API" persisted to disk)

I can’t say much without it being clear who it was, but a critical low level thing.

And the Sr was generally a very nice person who did not give much weight to levels, willing to engage with anyone.