You can assign the users to native applications by using cmdlets in PowerShell.
The following cmdlets assign a user to an application without roles.
$appId = (Get-AzureADApplication -SearchString “<Your App's display name>”).AppId
$user = Get-AzureADUser -searchstring "<Your user's UPN>"
$servicePrincipal = Get-AzureADServicePrincipal -Filter “appId eq ‘$appId'”
New-AzureADUserAppRoleAssignment -ObjectId $user.ObjectId -PrincipalId $user.ObjectId -ResourceId $servicePrincipal.ObjectId -Id ([Guid]::Empty)
More information about the command for assigning a user to an application role, please refer to the following article.
https://docs.microsoft.com/en-us/powershell/module/azuread/New-AzureADUserAppRoleAssignment?view=azureadps-2.0