Group not aligning to the part of object.
Please have a look at this video.
I believe the video will be more (easily) comprihensible if the expanded Layer is shown in full so the lower selected parts can also be seen,thus revealing the structure of everything.
You used the hollow arrow tool to select items. They might be part of groups such as masks or compounds. Use the solid arrow tool, and release items as needed.
Please have a look to new video.
I hope you will get my point this time.
The smiley is supposed to get center aligned to the selection only. But it is getting center aligned to the whole object.
Thank you for the video clarification.
I believe you can do it with least suffering if you:
1) Hold Alt/Option and Click the desired part of the Compound Path (to select it in its entirety), then hold Ctrl/Cmd and Click C then F then X then F (to create a new full path on top);
2) With the normal Selection Tool Select the smiley, then ShiftClick the new path from 1) and Click it again (to have it as the key object), then Align;
3) Delete the new path.
And I believe Mike was hinting at a way which in the actual case would mean that you release the Compound Path, then Align, then Make the Compound Path again.