I think i found where the problem lies of the codex entry for 'Harpy' not being unlocked if you fetch Agnimitra first and go meet the Harpy Matron.

[Papum]

As here stated this is the entry condition:

" Codex Acquisition​

Only one of the conditions below must be met to unlock the Harpies Codex entry:

• Having stepped into the Foothills and met the Harpy Matron "

Probably in the alternate Agni + Matron encounter version the unlocking of the codex entry isn't being applied.

Problem now is that it is an past event, those that have done it already won't be able to unlock the Harpy Codex entry normally for now.
Maybe in the future if we encounter her normally?