If you search for a navigational aid and then choose “add to route” it may add a completely different VOR that happens to share the same 3 letter identifier.
Example: I tried to add the VOR at “Tontouta (Noumea)” (LTO) to a flight plan. Instead, navigraph added ident: LTO Name: LORETO half way across the world.
This can be duplicated for just about any VOR with a duplicate name.