Getting Bigger return filing married-separately than married-jointly... Why is that?

For the past two years (2016 & 2017) we had a CPA do our taxes, I retired at age 60 in 2016 but my wife is still working.  We both felt that since I retired in 2016 it be best to allow the CPA to do our taxes since our incomes changed so much.  We were happy with the refund we were getting filing jointly.  In 2017 we had our CPA do our taxes again but since I had some additional funds taken out of my retirement fund the CPA found that we would do better filing as Married filing separately instead of jointly.

In 2018 I decided to do our taxes with TurboTax since the tax laws had changed so I bought the Deluxe CD.  I did the return Married Jointly  and Married Separately (for both of us) each time I itemized since we own a house and other deductions.

When I did I found that we did much better filing separately - over $1,300 better between the Federal and State?  Why would that be?  When I do the taxes separately I split up all of the deductibles (I took the mortgage interest, she took the property tax).

Did I do something wrong?  Does TurboTax have a way to determine if one way is better than the other?

Fred