If the system is applying different taxes to your invoices, follow these steps.
Step 1. Check your Purchase/Sale Type. If you are using a fixed tax rate and it is applying the wrong rate (e.g., if you have selected Local-18% but your item belongs to 12% tax category), it may calculate the incorrect tax.
Step 2. In this case, consider using Item-Wise or Multirate Purchase/Sale Type.
Step 3. Additionally, check the Item Tax Category. To do this, press Alt+M on the Item Master and verify the tax category.