While PKHeX has had legality issues since the new update, and I read that some people add a mon but it instead shows as lv 0.
Despite that, I've never had any issues of that sort. I was able to wipe my PC and fully inject various mons (for screenshots), so I have not encountered your issues, and have not been able to recreate them.
With that said, I am not denouncing any of the experiences either one of you had. Perhaps you guys adds mons differently from me.
By chance, your method happens to encounter the issue, so when you continue your method, you continue to encounter the issue.
As we're different people, I deviate from your method and unable to think up your method, thus never encounter it.
Thus, the only solution really was you guys to provide a step-by-step, so that I can try to do it your way, in an attempt to recreate the issue.