This issue could be caused by that the SID in the User Profile Service Application (UPA) did not match the SID in the User Information List used by the site collection.
You can try to update the SID of the User Profile Full table in the Profile DB. Here are two option for you:
First: delete all the of the problem profiles and re-import them
Second: update the user's SID in the User Profile Full table by using Move-SPUser PowerShell command (must be an administrator account)
For example:
$url = "http://www.example.com/" # your web application
$claimsAcc = "i:0#.w|contoso\user name" # user account
$user = Get-SPUser -Identity $claimsAcc -Web $url
Move-SPUser -Identity $user -NewAlias $claimsAcc -IgnoreSID
Please refer to the article that SharePoint: Users randomly lose permission – are deleted from site