It may be that this only happens immediately after jj git init.
But any tool that lies to people is a huge red flag. Because while I can memorize that caveat it's presumptuous to assume that an entire team of people new to a tool will remember a footgun. That's on the tool not the victims.
Asserting that `jj` "lies to people" is… probably uncalled for here. I'm not going to say it's impossible for the two commands to produce incongruent output, but knowing how they work it seems pretty unlikely. I think it's far more likely that either there was some confusion on your part (two different tabs in two separate projects?), you did something you didn't fully understand with a new and unfamiliar tool you were playing with (perhaps you misunderstood what `jj new` does?), or some other very reasonable and understandable thing occurred that falls pretty far short of "the tool lied to you".
Would you expect `git status` to "show you the changes, full stop" then?.
Where the hostility is coming from, ugh
Why is it so hard for people to even consider for a minute that they might be wrong or confused - nooo, this tool that was in development for years by at least one full-time google employee with a decade of mercurial dev experience and a ton of contributors, and that is loved by a lot of people already for it's simplicity and functionality - definitely failed in such a basic task, it's not you misunderstanding some basics in how it works, definitely, "full stop".
Another thing is that you might have set a `snapshot.auto-track="none()"` config and never told us, which is an opt-in way to disable autotracking, and which `jj st` does not support fully (if at all in released version) yet - then you totally "opted in" being lied to, sorry.