Hello there, I've been lurking for a hot minute and in leiu of introduction I have some thoughts!
There's a distinction here. Cliques, inherently, are not the problem. I don't believe this is what was meant in the original post, and I don't think this is what Ken was getting at either in early replies.
You have your default groups. Your staff, your premium members, your natural divides caused by badge and title. You also have a natural tone set by the earliest members of a new forum. This is natural, inevitable.
There is another sort of clique, one that forms independent of core group membership. These are subsets, coming about when a board is already established and has areas that 'run themselves' without staff pampering. Typically these are in forum games, formed among outside Discord Servers peering in, the natural breed of an autonomously active section, what have you. Positive or negative these rarely exist in a brand new or small community so you're more likely to encounter these if you own or participate in a larger scale forum, probably larger than this one. I think it also matters if the forum has a production focus - if it's for modding, roleplaying, some sort of creation with independent modules in the site. If it's kicking the can around it's not likely you'll get an autonomous area to form, and with it, an independent clique. But even 'forum game regulars' and 'rest of the serious site members' can be a distinction.
In the good case, these are groups that run autonomously and keep an area of the site ticking. A roleplay/RPG group that is dedicated and long lasting, a charismatic bundle of off topic bunnies, a handful of "producers" who've formed up a strong friendship. These often have a form of internal leadership, with natural followers and often a natural leader who has the loudest voice and is able to represent the group across the forum. But this is a fuzzy subject so it's not set in stone. It's the autonomous element that matters. The problem here for example is that staff might not be interested in this section. If Al is the owner and disinterested in forum games, perhaps this group forms without his awareness as he administers the rest of the growing board (with distinction!). Perhaps it is a group of "producers", I mean this broadly, who are into a thing that isn't well represented in staff. Groups like these often communicate among themselves and rarely need staff assistance. Perhaps they have their own Discord Server. They keep the forum popping off and that's what you want. But if you haven't kept tabs, if you don't have an element of staff to watch or better yet understand, or they've gone and formed an off-site group or they came as an off site group originally, you may be caught off guard when they fragment. You might not realize when your forum's value has lapsed and they decide to go somewhere else. A good thing gone bad. This is something you need to be careful of. Complacency will kill.
In the bad case such a group forms like above. But it is antagonistic, or stifling. It could be handful of members with a voice that drowns out others or leaves little room to disagree. Passionate, pedantic debators who are tiring to argue with but do not necessarily break rules, on a forum where their activity makes them the first thing newcomers will see (common case: generally chill topical server with a passionate political sideshow). A loosely united group against a distant, or unpopular owner or staff, probably with existing baggage or even inherited when a forum is purchased. A discord server with your forum's most unwanted, banned members and a handful who eagerly deliver the scoop. This I suspect is the sort of thing intended in the original post. I don't have a good answer as it's too late to simply keep tabs on them, now they are causing a fuss and you would be the asshole for striking them down simply because they disagree. Consistent with above they are typically independent, even alien enough that you're lucky to have a member of staff who's able to calm it down personally, or worse, a staff member is a part of this group and because they're also probably damn fine staff members who do a lot despite their rough edges. Again, generally an issue of communities at scale.
I'm interested in what people think of the bad case especially, when you're stuck with an unpleasant, hard to remove clique that you can't just appease with a few button presses. The best I've got is that you'd need to know the particulars and to deal with it case by case. You need to be willing to sit down, clear the slate and make compromises, or if the demands are not reasonable, cut the poisoned branches despite losing valuable workhorses in the process. The worst I've seen happens when the staff are in little position to 'just be more active' or their plates are full enough as it is. Indeed this is where it's at its worst - draining members on top of busy staff duties that erode staff morale to deal with but grows as a problem if ignored.
I think this thread so far has focused on easier, more wistful examples; obviously, your core staff and core members are not likely to culminate in these sticky messes. But they can and probably will form if you have a true bustling community. Of any sort - it's totally possible on Discord, and anywhere else.