Weapon gimmicks (special effects) are always recorded separately in the combat logs and so are talisman effects. Museum completion damage should be added to your own damage without a separate entry.
Furthermore, in this specific case Epherian was using Shattered Hellblade and Tenetur was using Razor’s Edge - none of these swords have any additional damage that adds 1-2k as a gimmick. And his Shattered Hellblade procs are listed correctly and separately in his DPS report.
As you can see from Vyxenne’s log I have mentioned it happens with Assault Rifles, Hammers and to the best of my knowledge with every weapon kind.
This issue cannot be explained by any of the things you have mentioned.
PS: One piece of additional information I can give is that this does not happen with damage from Passives. Likewise damage from special abilities of talismans/weapons are recorded correctly. This problem seems to occur ONLY while hitting with active abilities.