Unfortunately, in my categories (craft supplies) this kind of thing is quite common. I have made errors (most of which I picked up on not long after I've posted an order) but it started happening so often that along with keeping meticulous stock level records (so I can see if I have the right quantity remaining after an order has been sent) I decided to start taking photos of the addressed package, with all items that were picked and packed next to it. 

What I found was that I didn't make anywhere near as many mistakes as my buyers were having me believe. 

Now, when someone messages me and says they were missing items from their order, I can get visual confirmation of exactly what was sent to them, and I can work from there.

I don't ever accuse anyone outright of lying to me (because photos of what was sent doesn't 100% confirm what was received), I just reply and confirm that all of my records indicate that all items were sent, ask them to double-check the packaging for any items that may have been missed, and also ask for several other things such as the condition of packaging on arrival and so forth (if mail has been tampered with and items stolen, a police report needs to be made, though we all know that realistically, some unknown third party is unlikely to open a package, take a few items out, then send it on its way, but when you have proof you sent all items, the idea it will become a police matter can often result in the items being found in the discarded packaging after all). 

It is a total pain in rear to photograph every package that goes out, but it means I don't have to wonder or question anything and can move forward more decisively (anyone who messages re: missing items and I can see all items were sent is immediately added to my blocked buyer list, unless something else convinces me they're telling the truth - that happens less than 10% of the time someone cries 'missing items').