@Debbie930 I can understand their perspective as it might make them wonder if someone had left the eggs out, or contaminated the others by putting the shells back in.
I also include a lot of extras for my guests as I know from traveling how nice it is to have something readily available after traveling all day. Pre-COVID, we'd put out a charcuterie tray or something similar for late arriving guests (usually they missed a good dinner option and their eyes light up when they see it!), but avoided that during the peak of the pandemic. If anything, now we'll buy a nice pre-packaged tray and bring it out while showing them around so it's always sealed fresh. I always mention our experience of receiving nice amenities after a long day, and how we opted for packaged products for their safety. You kind of let them know you are going above and beyond for them and care about their safety.
Aside from a personalized welcome amenity, we generally limit anything perishable just so we don't have the worry of possibly missing an expiration date, or awkward situations like yours. We get around it by providing small size condiments, instant oatmeal packets, microwave popcorn bags, K-cups/creamers and other single use goodies. No worries about gunk on ketchup bottles or dirty hands scooping popcorn or coffee from a larger package. We even switched to travel sized tissue packs on the nightstands/bathroom instead of large tissue boxes (Kleenex, etc.) since that could be a virus spreader. We have shaving kits, toothbrush kits, and such on hand as well in case they forgot anything. Very few have ever needed them, but they all appreciate the thought.
If you want to keep providing eggs, perhaps consider cutting the carton to provide enough for a breakfast or two, while ensuring few if any leftovers. In most cases, guests will hit the local market for supplies anyway. All you need to do to make them happy is to provide enough to get them by until they go. If they got in at 11PM, the last thing they want to do is run out looking for a store to buy eggs for the kids' breakfast in the morning!
My response to the guest would be a simple apology that this was missed during cleaning and that you'll add detailed checks of all food items to your cleaning routine. Mention that you enjoy providing personal touches such as complimentary food and thank them for helping you to ensure the best experience possible for future guests.
It is a shame that someone left you a mess like that, but it does happen and we just have to take steps to prevent any future issues. Hope this helps!