In the invoice, even the total is correct, it keeps showing me this alert. "The line total amount is not equal to the item price times the quantity. Is this correct?" Is there any way to ignore this warning please? The total is same as qty x rate which seems like correct

You might get this if you're specifying all 3 values (quantity, rate, amount) and there are rounding issues. I would only specify quantity and rate and let NetSuite calculate the amount.