Ok,

I know I am late to the party here...  I have had the same problem with my QBO too.  This is a super frustrating problem because sometimes when you make an invoice for 7 items lets say, it will only raise COGS by 1 unit, and decrement inventory by 1.  So the only way for me to find this is running a Sales By Product report and scan the Margins and make sure there is nothing out of whack.

The system will fix itself if you go and change the invoice to a different unit amount, save it, and then go back and change it to the original amount.  If you then go to the product and run a report, you can see that then the invoice charges for 7, and inventory and COGS are affected by 7 as well.

This is a HUGE problem for me.  I have many inventory problems and this particular one is a broken system problem that falls well outside of the Garbage In/Garbage Out principal.  Intuit will always give you some excuse too like, oh you need to clear your browser cache, or they couldnt find anything.  But it happens, I have seen it happen numerous times, and its not ok.