If you have taken a property in the name of your wife, then she should be paying the EMIs. If it is on joint names then you bear your part and she would have to bear her part of the EMI.
If she alone is the owner, then the Income tax authorities will ask you whether you were paying the EMIs on your wife's behalf by gifting her the money or by lending the money. Also, if a person is paying the total amount of the EMIs in a year which is more than the exemption limit on income, the person has to show how he/she has received the income and file the IT return.
She should have filed her IT return. Please employ an IT consultant/CA and file her return, the consultant/CA can help you minimise the tax to be paid and fill the IT return appropriately.