MongoDB remove an item from an array inside an array of objects
You need to use the positional $ update operator to remove the element from your array. You need this is because "sections" is an array of sub-documents.
db.test.findOneAndUpdate( { "sections._id" : ObjectId("56fea43a571332cc97e06d9e") }, { "$pull": { "sections.$.registered": "e3d65a4e-2552-4995-ac5a-3c5180258d87" } } )