The article lists several reasons why the regimen is dangerous: if you get the bacteria that you're supposed to be getting, that bacteria will be continuously producing an antibiotic. Having bacteria constantly dosing you with antibiotics can lead to all the sorts of issues that long-term antibiotics present. Secondly, the article claims, probiotic manufacturing is very susceptible to contamination. Luckily, there are steps a manufacturer can take to avoid contamination, but it doesn't appear that this manufacturer is taking these steps.
All of this is stated in the article, if you missed this on your first read, you might consider re-reading it :)
Many bacteria produce antibiotics to outcompete other bacteria, though, so this isn't new or alarming information. Especially given that, as the author admits, the mutation that causes it to produce that particular antibiotic is naturally occurring in S. mutans!
It'd be a more interesting claim if it was argued that mutacin-1140 was particularly dangerous in the relevant doses (and this somehow never came up in the wild-type S. mutans that produce it).
All of this is stated in the article, if you missed this on your first read, you might consider re-reading it :)