[TRICK] Sometimes when I am not careful enough, I am getting that kind of problem with infill. This is usually because of very thin lines (because of small layer height) and high speed infill. If you don’t want to lower speed, another solution is to bump infill line width and infill rate, this in turn will increase flow during high-speed infills. (I am working with -dev version of Slic3r, but it applies to any software which allows you to change width of infill extrusion)
@Richard_Horne 's January blog post gets into the mechanics of this and more working with perimeter extrusion widths as well.