The same problem happens with internal hard drives that get mounted somewhere or are LUKS encrypted, see how this looks for me:
Basically, everything shows up twice but /boot (which is not encrypted)
But you can also see some of those items are greyed out, that happens when you right click items and select “hide item”. If you then deselect “Show all entries” in the panel options (i.e. right clicking on the headlines “Devices” or “Remote”) all of those get hidden and won’t get in your way.