Question

What made the spread of the bubonic plague especially hard to stop

Answer 1

The fact that medicine and the understanding of health was not developed enough for them to realize how the human body worked and so while they felt they were helping they actually were just making things worse, such as the bleeding out of people which was done because it was believed that if you were coughing up blood that must mean you had too much blood in your body so they cut people in order to drain blood and "balance" the fluids. Also many people made long pilgrimages of mobs everywhere lashing and whipping themselves because they believed that the plague was punishment from God and that by harming themselves was there way of trying to repent. However all this did was increase the concentration of people with plague in areas and that mob traveled all over allowing spread to be much easier. There was also the fact that fleas were extremely common and people only took baths like twice a year and that was considered being clean. So people had ticks and fleas all over their body so they did not suspect that being the cause. 
That's not everything but it is a little bit that can hopefully help.