This started off as a problem for me and while making the post on the Blender discord I actually figured it out on my own. Figured it would help someone. See below.
Basically to sum it up, animating with motion blur on, if you animate an object to scale to zero, chances are that frame with give you transparency issues.
Since I had initially keyed the scale to zero to have it disappear, I keyed the scale to a small value like .0001 and in the following frame I keyed the visibility to have it disabled in the render and that removed the motion blur transparency problem.
I also found that even though I had the object disabled from the render on the following frame, if the scale was still keyed to zero on that frame the issue would still happen. So best to scale to a small number and then key the visibility. Not sure if this bug pertains to just me. Running Blender 2.93.4 Rendering in Cycles.
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