How should that even be possible unless you scale the clips in some way? I'm afraid your approach makes no sense. AE simply doesn't adapt anything automatically. In your case obviously you would have to scale up the small clips to fit in a HD comp.
Ok and just to be sure (I'm new to this so thank you for bearing with me) scaling up, say, a 480 or 720 image to 1080 will result in a loss of resolution, right? Because that's kind of what it looks like now but I can't tell if I'm just doing it wrong ¯\_(ツ)_/¯
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Reading your question has me like
Whatever you scale up will depend on the quality it was shot at. It's about the resolution, so something that is 1080p can be viewed at any size and be lossless
Think of YouTube, you have normal, cinema, and full screen. The 1080p can be played in all the modes and look the same but a 360p will look crap on everything (worse on cinema and full screen.)