Hi awatkins, we may need your file and or screenshots (before and after) to try and replicate. Can share from CC files (https://assets.adobe.com/cloud-documents).
01 Screenshot before merging two geometries that are right next to each other
02 After merge showing layer that is the size of the artboard, rather than just the two geometries
03 After I turn layer off and back on, I can see additional pixels that have been added to the layer, random boxes that are not representative of any artwork in the file - typically white as show here but sometimes have color in the cmyk range
Would you be willing to share the file in question so we can trouble shoot with it? You mention Artboards in your commented screen shot, does the file have artboards?
Here's one of the files that has been having issues. Has been happening on any file since the last update. And sorry, maybe I shouldn't have mentioned "artboards", just referring to the artwork.
Just wanted to give this thread a bump. I have merging problems on every PS mobile (ipad) project I've ever had. Sometimes the option to merge down isn't available, and then it appears after you "merge all visible" and undo it. Sometimes when merging down big white squares appear in the merged layer, which then have to be erased.