I also experience this. I have not tried his exact steps, I will explain how it works for me.
It has happened for as long as I've used music bee. It is not something new.. many years old.
I drag files to the inbox.. then I tag them and drag them off to either "Music" or "Audiobooks" tabs
they all disappear from the inbox.
Then more often than not, when I drag more mp3s into the inbox, one (and only one) straggler will reappear in the inbox, along with all the new files.
I cannot be sure if the file ever appeared in the moved location before popping back into the inbox. I think so.. as I don't actually scrutinize each song's name, I do sometimes look at the track numbers.. and would notice if a song is missing.. what is for (fairly) certain is that any tag that is applied to the album in the moved to location (music or audiobooks libraries), including photos, will not be applied to the mp3 file when it pops back into the inbox.
I stress that there is only ever one straggler that pops back. I have seen this happen hundreds of times. There is never more than one. Also it is sometimes possible for 0 songs to pop back into the inbox the next time I add mp3s there. However once it starts happening, most of the times I add songs will result in a straggler popping back in from the previous batch of songs added.
I always (100% of the time) will update some tags, usually in batch edits, of songs that I drag to the inbox when I add them to the inbox, before dragging them to the Music or Audiobook tabs. I wouldn't have mentioned this except I read that the OP mentioned that he usually edits tags.
When I say I drag songs to the inbox, I mean from outside of MusicBee as a way to add them. I cannot remember if stragglers can appear when adding songs through scanning the library, which is a method that I sometimes use as well for adding songs to musicbee.
update: yes it happens on library scan as well
update: I can confirm that after I drop an album in the inbox, then drag it to the music folder... then in the music folder select the album and paste artwork, that when the straggler appears in the inbox later it will be without this artwork. I am still not certain if the file was actually among the files in the album I selected or was missing. But for sure the straggler was not at that time visible in the inbox. So this might mean that the file is actually left in the inbox and just not displayed for some reason until the next time files are added to the inbox.