There are a number of possible reasons for this
1) You don't have concentric infill selected (may help)
2) If the gaps between the perimeters is not a multiple of the extrusion width then it cannot infill with a single extrusion and will create a wavy infill. Eg. if the extrusion width is 0.4 and the gap is 0.7 then it can't lay two full extrusions, so it will have to fill the gap with a wavy fill or there will be a remaining gap.
I hope that makes sense.
NB. I know it's always said, but attaching a factory file would make the problem easier to diagnose specifically.