Spanning Tree Protocol sees an EtherChannel as a single port. This presents a danger of creating forwarding loops if channeling ports are not consistent on both sides of the channel. Cisco has developed a special mechanism to detect and disable channel inconsistency to prevent packet duplication, looping, and other issues associated with inconsistent EtherChannels.
Check this URL:
http://www.cisco.com/warp/public/473/127.html