Sounds like your top thread was not working properly. Perhaps the thread slipped out of the take-up lever, then lack of tension & all that extra thread underneath got tangled up. Also sounds like you did the right thing to "fix" it. Taking off the throat plate is not likely to void the warranty, since most machines now have changable throat plates for different types of sewing.
How about embroidering a very small motif over the hole. I'm thinking tiny flower or ladybug, etc.