The issue is that several things are only computed every five days, in particular research projects. When you advance by 1 day you might not enter the next production cycle, so no R&D progress will be computed, and thus not R&D points will be added to the project in question, hence no project completion. That is not really "broken", it's just that R&D only gets computed every five days. If you advance by 1 day, five times you will see the research being completed.
So in a way the thing that is actually slightly broken is the estimated time that the R&D will be completed. The calculation for this time treats progress as continuous, even though it is not. Personally I can live with that, R&D should not be quite so deterministic anyway.