Assuming that your store has been checked for proper pixel installation and making sure there are no other apps or code snippets that are causing duplicate pixel actions:

When you use multiple FB Pixels or use the same pixel in multiple stores and/or using multiple overlapping Custom Conversions, FB reports can seem to be over reporting compared to actual Shopify sales.

#1: Facebook reports are not meant to accurately reflect your Shopify sales. You should be using different tools to capture all sales, Google Analytics for example.

#2: FB reporting indicates the conversion participation of your ads. That's due to the default attribution setting of 28-day click-through AND 1-day view-through conversion attribution. What that means is that - for example - a sale can show up in a report if the user viewed a paid impressions of an ad post (not clicked on it), and within the next day clicks on an organic impression of a post that sells a product in a different store that's tracked by the same FB Pixel. Then that sale (although in a different store) will be reported in the ad for the first ad that was viewed (because it was a paid impression and the sale in the other store happened within the default attribution window.
​

You can try to "correct" this by a number of different actions (remove the 2nd FB Pixel, not track actions in different stores with the same FB Pixel, not use Custom Conversions and 2 FB Pixels at the same time, etc...) However, this would just be trying to make FB reports reflect Shopify sales which they're not meant to do anyway. So, we think it's the better course of actions to gain knowledge and experience with these types of reports. When you do it will actually help you understand more about your ads and evaluate them better.