I have studied intensely under perhaps the main proprietor of the opposition to Yersinia Pestis as the cause of the Black Death, Samuel Cohn. There have been ongoing challenges for years for a number of reasons.

First is the problem of speed. Yersinia pestis has to go through a complex process (involving fleas) in order for it to be contractable by a human. Given the speed at which it travelled across Europe and the lack of integral proponents in this necessary process, it seems highly unlikely this would be possible. Also, when observing modern cases of Yersinia Pestis it was found to be far slower in transmitting (largely due to the complex process) and spreading across a group of people than occurred in the Black Death.

Second is historical sources. Many of the most reliable historical sources of the time, such as Giovanni Villani, had concise scientific reports of the symptoms of the disease. Many of these sources, despite never discussing or comparing notes (due to being on opposite ends of Europe) had precisely the same reports of symptoms, none of which align with modern day symptoms of Yersinia Pestis.

Third is demographic data. There were multiple stages to the Black Death and each time less people died. By the end only the children who had not experienced the Black Death before contracted the disease, suggesting the older generations had formulated a resistance to the bacteria. This is impossible for Yersinia Pestis.

A few years ago, however, traces of Yersinia Pestis were recovered from a corpse that had died during the Black Death. This largely silenced the main opposition, although it sparked a new debate of how the same bacteria could have had such drastically different effects. Some have suggested the bacteria has mutated over the decades.

I hope this has helped somewhat, please dont hesitate to ask any more questions.