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Perhaps i'm designing my shapes or design wrong...but here is the process and problem
When i have two shapes i want to join, either a long rectangle and a slanted edge, there is a slight choppy/pixelated effect and looks like one of the shapes is lower or out of position then the other, even though they are on the same axis and otherwise the same height, etc.
I have a few images that show it (blown up screenshot) and the outline (cmd Y) before and after the unite function is used.
No changes to my settings, using the latest Illustrator 2020, iMac 5K. no anti-aliasing or low res document (300ppi) this has happened on other verisons and Mac systems.
This can be replicated if you have two squares or rectangles and have them side by side or overlap and unite them using pathfinder (shown below)
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So I assume there is not issue with precision of your artwork?
Ho is your pathfinder set up? There are options in the panel menu. Do you delete excessive anchors?
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there were no additional anchors, and even if you took two new squares for example, i could replicate the issue.
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It may look like that due to the difference between "GPU Preview" and "CPU Preview".
Is not it?
To switch to CPU Preview, choose View > Preview on CPU.
To switch to GPU Preview, choose View > GPU Preview.