This is not quite reproducible, but it has happened a few times:
If I start typing a name (e.g. "debug"), then partway through the list of completions pops up. If I'm typing very slowly, this happens after "deb". Sometimes, not always, if I continue typing because I didn't notice the popup, something weird happens: for this example, the "u" appears after "deb" in the console window, but the cursor is positioned before it. When I type the "g", it is inserted in the wrong place, so I end up with "debgu".
Once this happens once, it is easily reproducible in that session. However, I'm not sure what triggers it in the first place.
I tried briefly testing with your noted steps but unfortunately wasn't able to reproduce.
Some things worth asking:
Does it reproduce in both the Source window and the Console pane?
Does the issue reproduce for you in all files within that session, or only certain files?
Does reproducibility of the issue seem to depend on the content of the files, or is it independent?
Any possibility it could depend on which R packages are loaded in that session? (in case they're exporting symbols seen and used by the autocompletion engine -- seems unlikely that this could be the cause but worth asking anyhow)