Dr. George Heinze and Dr. David Firth (at Warwick University) has focused on the quasi-complete seperation at Logistic regression analysis when cells of zero in two way, or three way classification were found. You must apply Firth type Logistic regression (Penalized Maximum Likelihood Method) to your data.
Please see my paper related to this topic: http://journals.mui.ac.ir/jrms/article/view/2206
In fact, I recommend you to contact Dr. David Firth.