Try this fix.
1-) Open Dolphin and Make sure you are using the DirectX9 Plugin
2-) Click Browse
3-) Pick the Folder that your Game(s) (includes metroid prime) Exist it
4-) Once you are done , Right click on metroid prime game banner on your dolphin browser
5-) Click proprties
6-) Make sure the mark "Check" on "Safe Texture Hack"
7-) Press Ok
8-) Run the game
Hope this helps
it also helped me to use the Bloom hack using DirectX9 Plugin
I don't have Metroid prime but in the open GL options the Safe texture hack says it can be used to Stop the crash of it and DX9 can use open GL Tools using the browser.
and The DX9 Can Use other Open GL Hacks too , if you boot it from the Dolphin browser.
and sorry if I am lazy to Spell the game right XD
1-) Open Dolphin and Make sure you are using the DirectX9 Plugin
2-) Click Browse
3-) Pick the Folder that your Game(s) (includes metroid prime) Exist it
4-) Once you are done , Right click on metroid prime game banner on your dolphin browser
5-) Click proprties
6-) Make sure the mark "Check" on "Safe Texture Hack"
7-) Press Ok
8-) Run the game
Hope this helps

it also helped me to use the Bloom hack using DirectX9 Plugin

I don't have Metroid prime but in the open GL options the Safe texture hack says it can be used to Stop the crash of it and DX9 can use open GL Tools using the browser.
and The DX9 Can Use other Open GL Hacks too , if you boot it from the Dolphin browser.
and sorry if I am lazy to Spell the game right XD