thanks for the advice. I do have the stock management selected on the general settings. I disabled the pos plugin since my count is off anyways. I went through logs and could not find anything suspicious.
I have installed the activity log and started keeping an eye on it. I have my products in categories for easier shopping. Some products are listed in bundles and composite so the base product is hidden on the site. I use a category labeled inventory count for this. I have all those products set to visibility on site : hidden. That category keeps being added to the site with the products then being on shop and search results. The activity log does not show anything making this change. It just suddenly changes. This is with the pos plugin disabled.