Metroid Prime Log Book

After you scan both forms of Metroid Prime, is there any way to keep there scans in your log book???

No, there is no way of doing that because you can't save.

But the game saves after the credits.

I think it only saves some things because i have all the scans and the Metroid Prime doesn't appears anywhere.

You cant save the scans of Metriod Prime v.1 or 2 because they lie at the point of no return so you cant turn back. However, if you are trying to unlock one of those image galleries by scanning everything, and Metroid Prime's scan info is the last one you need, then you'll unlock the gallery, but when you start the game again (same file, after defeating Prime) your log book still will not have them saved.

i think the game registers that you have scanned them... but it just doesn't appear in your logbook... it might right after you scan, you might wanna check that.