I have not seen reports here of a glitch where Apple is taking purchases out of your account when they do not show up in your Purchase History. That would seem unlikely. What is the exact description of the charge you see on your billing statement?
What could have happened is that your card has been compromised and you would need to dispute the charges with the bank that issued the card. This happens frequently when the physical card has been used at a retail terminal where a scammer has installed a shimmer/skimmer to read your card details. Since you do not see the charges in your Purchase History/Subscriptions, this is likely what happened.
The other possibility would be when you use Purchase Sharing on a Family plan and the charges would appear under the Apple ID of the family member.