TDS on Rent

I m not too sure about this but as far as i remember upto march 18 tds provisions were not applicable for organisations registered under 12A

You can deduct the TDS now also before filing the Income Tax return and pay it out of your pocket with interest. Thereafter you can claim the expense in the Profit and loss account by grossing up the whole amount

already filed the Income Tax Return for 17-18

You can then try and take a CA signed declaration from the individual ( to whom u have paid rent) that he has included this income in his income tax return and paid tax on it. But u have to ensure that he has filed his income tax return. if he has not filed then u can't take this stand.
You will then have to pay interest on TDS not deducted from date of deduction to date of return filing by that individual