Pawel,
A physical interface can be part of several different pieces of your config; a simple L2/L3 port, a port channel, VE interfaces, etc.
If your Physical port is part of a trunk mode port channel that has associated VEs configured, the ACL is most likely configured on the VE. This is what the error means when it states "Interface Hierarchy" as the port is associated to a "hierarchy" of config PHY > PO > VE
code:VDX6740(config-Ve-10)# do sh run rb 12 int ve 10
rbridge-id 12
interface Ve 10
ip access-group TEST001 in
ip proxy-arp
ip address 10.10.10.10/24
no shutdown
VDX6740(config-Ve-10)# ip access-group test001 in
%%Error: An ACL is already configured on this interface or interface hierarchy.
Michael Morey
Principal Technical Support Engineer
Extreme Networks