But there could be a matter of difference in both the cases.
Like if the date of invoice is taken into consideration, there could be difference in stock tally.For eg. you receive a invoice dated 24.05.15 and you consider this date as your purchase, your stock will increase in your books of accounts but you may receive the materials some days later. Hence, your physical stock may be different from your book stock.
On the other hand if you consider receipt of material as your purchase date, you may have a mismatch with your seller's statment. For eg. a seller has billed you with the invoice date 31.03.16 and consider the same date for his sale entry, but you receive the materials on 03.04.16 and you consider the later date for your purchase entry. As in this case both quarters and financial years have changed, you may encounter the difference with your supplier in both VAT Return and Audit Reports.