The guy wasn't charged for pointing out "this isn't a miracle". He was charged for following it up with a series of accusations -- claiming that it was a scam set up by local priests (defamation), and making comments about how religious people are "gullible", "regressive", "irrational", etc. (provocation). He went well beyond debunking and into the realm of conjecture/speculation, and ended up violating a number of local laws by doing so.