slic3r issue

I just assume situations like those are when the gap is too small for another bead of filament.  In the case you posted, though, I wonder if shifting the whole in-fill by half a bead width would have worked, i.e., filling in both gaps with a single bead.  I would guess it's a slic3r shortcoming. Sometimes, I've increased the perimeters by one and it eliminates the problem, but I only did it a couple times because most often, the toolpath is very different across all the layers of a job, and the fix for one or a few layers causes problems for others.