I can reproduce this. It happens when you visit the site with network.IDN_show_punycode = false, then set it to true and visit the site again. You now have two History entries for the same site with different URLs which are actually the same URL, only one of which can be deleted.
I finally managed to delete the remaining entry after switching the preference back and forth several times and re-visiting the site each time. There's probably a slight database glitch in places.sqlite for these cases.
I went back to Firefox 60 and played with the punycode setting and deleting History items. I was unable to get two copies of the URL to show in History. I also had no issues deleting the History entry even when I set the punycode setting to one value, visit the site, change the punycode setting back, and try to delete it.
There might be a (albet small) bug here somewhere, or my testing wasn't good enough.
I don't consider this a major enough issue (especially since there is a straightforward workaround) to put in the worklist, but if the relevant patch on Bugzilla is found by someone(tm), I'll see if it can be adapted to TenFourFox.