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I wanted to find the elevation difference between 2 DEMs. When I got the data, I had to georef one image and had to aggregated it too because their cell values do not match. I also tried to resample but I read that aggregating it is better. After much tweaking, I then subtracted them, but the resulting DEM looks like a hillshade. What does that imply?

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It is hard to tell without an image, but this is probably due to a shift in plane coordinates. e.g. If you have the same mountain shifted toward the south, you will systematically overestimate the height on the South face, and underestimate it on the North face. So you end up with darker areas always on the same face.

A good way to check for shift is to create a composite image with your 2 DEM and display it in RGB (DEM 1 for 2 chanels and DEM 2 for the third channel). If you have colored fringes, you have a shift.

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    I had this exact issue when resampling DEMs and then creating error (difference) maps. I think the problem occurred with both bilinear and cubic resampling but unfortunately I can't remember how I resolved it.
    – pvdev
    Commented Mar 6, 2014 at 12:50

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