Removing AccessRights - WARNING: An inherited access control entry has been specified and was ignored - WARNING: An inherited access control entry has been provided and was ignored

So this just happed:

Remove-MailboxPermission -Identity SharedMailboxAlias -User Username -AccessRights FullAccess -InheritanceType all

Confirm
Are you sure you want to perform this action?
Removing mailbox permission "SharedMailboxAlias" for user "UserName" with access rights "'FullAccess'".

[Y] Yes  [A] Yes to All  [N] No  [L] No to All  [?] Help (default is "Y"): y
WARNING: An inherited access control entry has been specified: [Rights: CreateChild, Delete, `

ReadControl, WriteDacl, WriteOwner, ControlType: Allow]  and was ignored on object `

"CN=SharedMailboxAlias,OU=Shared Mailboxes,OU=Mail,DC=Domain,DC=lan".

Checked to see what was keeping me from removing the access rights:

Get-MailboxPermission -Identity SharedMailboxAlias -User UserName

Identity             User                 AccessRights                 IsInherited Deny
========             ====                 ============                 =========== ====
Domain.lan/Mail/S... Domain\UserName      {FullAccess}                 True        True
Domain.lan/Mail/S... Domain\UserName      {FullAccess}, Delete...      True        False

And there it was, the "IsInherited" value True.
So its coming from above...

So I had to go through and remove some legacy permissions from Exchange. This can be added at multiple levels so it’s aways a diagnostic trail to where this was added. Go through each of these and if IsInherited is set to False you’ve found out where it’s being applied from.

Get-MailBoxPermission Domain\UserName

Get-MailboxDatabase | Get-ADPermission -User Domain\UserName

Get-ExchangeServer | Get-ADPermission -User Domain\UserName

Get-OrganizationConfig | Get-ADPermission -User Domain\UserName

Remove the Permissions per level with

Get-MailBoxPermission Domain\UserName | Remove-ADPermission

Get-MailboxDatabase | Get-ADPermission -User Domain\UserName | Remove-ADPermission

Get-ExchangeServer | Get-ADPermission -User Domain\UserName | Remove-ADPermission

Get-OrganizationConfig | Get-ADPermission -User Domain\UserName | Remove-ADPermission

Some of the permissions where also added from AD.

Open up ADSI Edit and Navigate to these :

In “Default Naming Context” OU=Microsoft Exchange Security Groups,DC=Domain,DC=lan
In “Default Naming Context” CN=Microsoft Exchange System Objects
In “Configuration” CN=Microsoft Exchange,CN=Services,CN=Configuration,DC=Domain,DC=lan

Make sure the user is not in any of these.
After the User has been removed from any of these places its inheritance is gone is no longer listed.