Stock count differences occur, that’s part of the nature of the inventories and the procedure – to identify if any of the positions differ from the physical count.

It’s what you do with the results afterwards that matters. 

One thing is obviously making necessary adjustments in accounting. The results are not just to take as a fact but as a fact that your accounting reflects inaccurate data. Making those adjustments is crucial most probably also for your production department if you happen to have one so they’d know what they have in stock to use and for your sales department so they’d know what they can sell. Having accurate positions is therefore quite necessary. It’s the reason you make stock counts in the first place.

Another thing that’s more profound is the understanding why those differences occurred and if anything in your company’s internal processes or controls needs to be changed. For an example if some items are constantly taken into stock in wrong amounts, maybe some instructions are in order or if some items should be kept in bigger or smaller units (if they’re packaged) etc. It all depends hugely on the type of the specific item, but do make notes if the differences are noticed – maybe something could be changed in general processes so that the differences in this specific area would occur less.