I just started using XD and spend way too many hours on this problem. I tried many different things but i can't figure it out. Please ignore the text on the squares, since I thought I found out the problem is reproducable but it kind of isn't.
As you can see, I cant get a clean Autotransition because the main square is not covering up every other element that is acually in the background or beneath the moving square.
Also tried grouping the quares that have to stay the same size in order to not overlap the growing square.
Thank you for reaching out and sharing the screenshot and the video. Would you mind sharing the file with us here so that we can test at our end? You may upload the file to a shared location such as Creative Cloud app or Dropbox and share the url with me over a private message.