The wonders of iCloud. It “just works” … or it doesn’t. When I was using it for my main Obsidian vaults I never had any problems, but I’ve seen a bunch here.
In the Files app, try tapping on the ones with the cloud icons to force a download. A restart of the phone might also help.
Also, your iPhone has plenty of free space, yeah? Sometimes iOS/iCloud will try to be “helpful” and offload things to iCloud if storage space is running low.