Since transubstantiation (the belief that the bread and wine turn into the blood and body of christ during communion) is probably the most believed miracle (since all Roman Catholics believe in this), I'll simply say that there has been no evidence for it. Transubstantiation hinges on the idea that, when someone drinks the wine or eats the bread, the physical properties of it don't change; they both still look, feel (and if you analysed them chemically, they'd still have the same chemical composition) the same. However, they still change to then contain the essence of Christ. The issue with this is that it has zero scientific evidence. It cannon be proven. And if it's possible to say something with zero evidence, it's also plausible to reject something without evidence.

Now, you might be referring to eucharistic miracles, including but maybe not limited to: a priest went to the house of a very sick man. He told the sick man's family, when he vomits, collect the vomit and put it on a fire. They did so, and once the fire had died down, the Host (the bread/ body of Christ) remained unscathed.

The first issue with stories like these is that they all come from a time period very much long before the birth of science; perhaps the birth of science has resulted in the death of miracles, since nearly everything has a scientific, rational explanation.

The second issue is that we have magicians today (Dynamo, Derren Brown, David Blaine) who, in the ancient world, could have been called prophets or messiahs. Because Dynamo has walked on water, David Blaine has floated into the air and Derren Brown has done much deeper, psychological illusions; all of these things would presumably have been classed as "supernatural" before the time of science. But today, we know for a fact that these three examples are just illusionists. Why couldn't other miracles be just the same? Why is it that these miracles are only witnessed by the least literate and least educated people from hundreds, if not thousands, of years ago?

We don't have to "debunk" eucharistic miracles. The sheer lack of any physical evidence has done that for us.