It could be the hotel refilling bottles, or it could be previous guests if they aren’t checking the seals.
I was staying at the Marriot Back Bay in Boston a few years ago. I pulled a Heineken out of the mini bar and took a swig. I immediately ran to the bathroom and spit it out into the sink. Thankfully, it was only water. A previous guest had drank the beer, refilled it with water and twisted the cap back on. I left a note for the maid, but still got charged for the beer.
I guess this is why some fancy hotels have gone to electronic sensors in their mini fridges to keep this type of thing from happening. You get charged as soon as you remove something from the slot in the fridge.