The only arguments I’ve heard against them are:
“That’s just not possible.” This misses the point of calling it a miracle.
“It’s just mold.” There have been a couple potential cases I’ve heard of that wound up being mold, but once that’s discovered they are no longer held up as miraculous.
“The priest switched out the Eucharist with something else to fool people.” - While you could technically claim this against pre-scientific miracles, modern instances of Eucharistic miracles have been examined in double-blind studies and proven to be genuine human tissue. What’s more, the blood types have been consistent, and at least two studies have found that the flesh from the miracle is from a human heart under extreme duress. The fact that modern miracles can be shown to be real lends validity to historical miracles, so I don’t buy this argument for most cases.