In S03E12 of The Walking Dead when Morgan and Rick cross paths again and Rick tries convincing Morgan that they know each other, Morgan exclaims that there are people wearing dead people's faces. IIRC there wasn't a showing of this kind of group/people though until all the way in Season 9 with The Whisperers.
Probably not a deliberate one...
As I recall Morgan had been hallucinating in that episode so it's possible he was referring to that.
Even the actor and producer weren't sure so it seems unlikely that this was an intentional reference, more a happy coincidence.
So was Morgan referencing the Whisperers?
Lennie James, who plays Morgan on the TV show, said that he didn't know.
"In all honesty, I couldn't tell you," he told ComicBook.com. "That's not to say that it's a no, but it could be one of those where it happened [and] it's just that [executive producer Scott M Gimple] hasn't told me yet.
"So, in all honesty, I can't answer that question because I don't have that knowledge."
So what does Gimple have to say?
"That definitely predated my knowledge of the Whisperers, because they were not at all in the book yet. Maybe that could wind up being a reference," he said.
"You never know. Even though it predated my knowledge of the Whisperers."
The TV series was originally based off the comic, but at some point the series went in its own direction. The thing about TV series is that usually, after the initial 6 or 12 episodes are written, the show begins to be written the week before it's filmed. This is for a number of reasons, whether it be because they don't know if the show will be dropped or what have you, but typically it's written and rehearsed one week and then shot the next.
There was no source material for The Whisperers in Season 3. Morgan is still in shock at that point, seemingly hallucinating and having a difficult time separating the horror of reality. "People wearing dead people's faces" was most likely his perception of the Walkers, how they're dead yet "alive", animated yet looking like corpses.
Although I can't think of any other examples off the top of my head (I pretty much just woke up), I know this isn't the first time I've seen a show where a concept from an earlier season gets re-used or expanded on, and this was likely one of those times where one writer probably went back and thought, "Morgan said this once, we should create a story arc where people literally wear dead people's faces".