From what I understand (Both from seeing other Ninja's and myself) Doton at odd times (During boss fights) tend to be because of a mistake in Mudra combination

Whether this be due to mis-timing, lag, or other, will usually result in Doton being placed down, an example would be activating Huton via: Jin - Chi - Ten.
Start with Jin like usual, and then go through lag, or some other form of timing where Chi is not registered and I instead get Ten, which would give me the Katon icon, now realizing what I've done, I've effectively missed Huton and can either do Katon, Bunny, or Doton, so I'll move on to Doton and just place it down instead of wasting the Ninjutsu.

Just posting my experiences as to why Doton is placed randomly at times, yes you may call me a baddie or whatever for this. :C