It starts with basic things, like objects stuck in places where pikmin are unable to find a place where they can reach them (like a dead bug too close to a wall). That sometimes happens even with fruit that hasn't even been touched yet, making it difficult to pick up that fruit and suggesting that some QA corners have been cut before release.
Then there's stuff that happens less often, like when I killed a big enemy in a tight bridge-like space - this was on the Corroded Maze map, where a Bulborb sleeps on such a bridge close to your base. When you kill him, his body might end up slightly to the edge of the bridge, and when your pikmin attempt to pick him up, they will, of course, take a moment before realizing which way they need to go. What happened was, they wandered even more to the edge, which made the Bulborb fall off with all the pikmin I have assigned to picking him up. After a few seconds, the dead body respawned, but the pikmin were, of course, lost.
Another annoying bug was related to squad management. In the heat of a battle, I had several pikmin left in my squad once, but wasn't able to use them, presumably because they were stuck in a Medusal Slurker or something. When that happens, or when your pikmin get stuck behind a wall somewhere, they are typically removed from your squad until you're able to reacquire them. Trying to use pikmin that you're supposed to have at your disposal but actually don't can be quite confusing and in this case, it cost me the match because I panicked and it took me too long to regroup.
Before getting Pikmin 3 Deluxe, I've been playing the original Wii U game in Bingo mode for years, and I don't remember ever encountering any of these issues during that time, perhaps with the exception of fruit being sometimes a bit tricky to pick up. I've only played Bingo in P3D several times so far and I'm overwhelmed by the lack of polish. I'm still going to play that version going forward because, quite frankly, taking a Switch with you to a friend beats having to pack a Wii U, but it's a bummer.