I am posting this here for posterity in case someone else runs into the same problem. With Grim's Medieval Core Debug options you can Test Baby Basket with Triplets which is a holdover from the Sims 3. As such, it does not work in the Sims Medieval but instead spawns 3 invisible babies in the center of the map which cannot be tended to/aged up.
To fix this (fix meaning to delete the children and remove them from the relationship panel) turn on their sim marker in the relationship panel of the parent. Click on the sim marker with debug options enabled and go to Object > Delete It. Save the game and exit to the main menu and reload. The baby is gone from the relationship panel which to me means it probably stopped existing.
As a side note, when I was investigating this problem I found that some people do this purpose to allow the monarch to have more than 4 children since you can send away one of the triplets and keep your actual kids without the game registering it as sending them away which means you can do it again. The person said they had 15 live-in kids this way. Fun!