Can cited works hold grammatical positions in sentences?
Conceivably the reviewer objected to the non-mention of peoples' names, thinking that should write "guided by J. Doe [12]" or "guided by [Doe12]" or "... by [Doe2011]"... Something in that direction would be my preference, also, since numbers in a bibliography are completely artifactual, not really adding any information. Names are far more informative.

But, still, it's possible that the objection was completely stylistic, so ... "it's just a rule"... which means rational discussion of it is presumably out-of-bounds. Such things seem silly to me, but I am acquainted with people for whom such rules are the only defense against Darkness and Chaos, etc.

I'd not comment on such things in any review/referee-report I wrote, but I can imagine some might. The operational point probably is that if the referee chose to mention it at all, it means they do have that particular fetish, so just comply if you want approval. But don't "pass it on", if you were to ask my opinion... :)