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I figured out what this is. If you select digseed while over a planted plot, and then return to the seed select screen immediately, it thinks you had a slightly different seed selected when you enter the seed selection menu (that is not digseed), so it plants it while the seed selection screen is up. Regardless of what you selected, it has already planted a different seed. I think that seed is in a particular slot (maybe the one right before or right after digseed? I'm not sure), because it's consistent across a run (on one run it was always cloak, on an other it was always vert laser, etc)

awesome, i've been wondering what that was about, it happens to me as well. thanks for the details/sleuthing on this!