Personalised aspects within after effects are often placed in precomps. Those precomps are then placed within other precomps, and so on. Try to make sure that the scaling of all these compositions remains below 100%. If you scale above 100%, you lose quality, even if the composition above that scales it back down to below 100%. As soon as you hit scaling above 100%, no matter other scaling attributes, you lose quality.
You may not notice this in a high quality master after effects file, but in the lesser quality and lesser resolution of the final output this is certainly something you can see and notice. Try to avoid this at all cost. As soon as you have to scale something over 100%, please try to think of an alternative. (unless its for a quick movement where quality isn't an issue, like quickly zooming out for example.)