Can I deduct office expenses from a sale commission invoice? it is deducting the expenses from the total sales amount. It is not crediting the HST with the taxes.

You should be able to create a product/service for Office Expenses, and link it to your Office Expenses category on the COA.  Then enter as a negative line, with the appropriate tax code on that line.  Then your total HST on the invoice will be reduced by the amount of HST calculated on the negative line.

The net effect of this will reimburse expenses (reduce) on your financial statement for the amount of that line and not affect your income accounts at all.

I'm not sure if this is what you're referring to.  It isn't clear whether you are talking about a sale commission invoice that is coming to you from a vendor or a sale commission invoice you are giving to your client.