I can't open the model, so I don't know your situation, but often you can makes things work if you mirror or pattern bodies instead of features. That means you have to build things differently, but sometimes I find it's the only way.
You've selected boss extrude and cut extrude as well for mirror and hence getting the issues. Also the fillets won;t get mirrored as well. So you've three options:
- Mirror the cut extrude 2 and then fillet on both sides.
- Use Dwight suggestion of modelling the half side and then mirror body.
- Create the model using a revolve feature and single sketch and then fillet.