Can you clarify what is the exact request you are making? To grant permissions to specific item(s) only, you need to use the following request:
POST https://graph.microsoft.com/v1.0/sites/{siteId}/drives/{driveId}/items/{itemId}/permissions
{
"roles": [
"write"
],
"grantedTo": {
"application": {
"id": "xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx"
}
}
}
Note the use of grantedTo facet instead of grantedToIdentities which you'd use for Site-level permissions