This happened to me several times in the Supreme Masters draft league. In my first draft (for reference, Match 1 had ID #263975333), two extra copies of Cryptic Spires appeared in my deck when I added basic lands, and I was unable to save the deck; I got an error message along the lines of "the contents of this deck aren't legal in the format". The extra copies went away when I closed and reopened the deck builder. This same issue has occurred for me in another Supreme Masters draft as well.
In addition, during Match #263979832, I added a basic land during sideboarding while having a Cryptic Spires in my maindeck. An additional copy of Cryptic Spires appeared in my deck. This meant that I was unable to make changes during sideboarding, because whenever I tried to submit the modified deck (even with the extra Cryptic Spires not being in the maindeck) I received an error message saying: "An error occurred. Some cards that incorrectly appeared in your pool were detected and removed." The extra Cryptic Spires was not actually removed after this message was shown, so I was not able to make sideboard changes.
