Alpha Channels and Premultiplication
One major source of confusion and even derision for AfterEffects has to do with its handling of alpha channels and
premultiplication. After Effects has a persistent concept of
the alpha channel as part of every image, and this channel
is expected always to be unmultiplied within After Effects,
whether it originated that way or not.
Any color multiplied into edge pixels is to be removed
upon import (in the Alpha section of the Interpret Footage
dialog), and reintroduced only on output. Provided those
Alpha settings are correct, this works surprisingly well, but
at some point you may need to better understand how to
take control of edge multiplication within After Effects.