1) Monsters have allies that aren't fully loyal. These monsters might initially be unfriendly to the PC's, but can be won over by parlay - or might seek to parlay if the combat goes against them.
2) Monsters have slaves or servants who aren't fully loyal. These monsters might serve out of fear, but would be willing to revolt in exchange for freedom and enough gear to survive on their own. Alternately, they may just want to serve the strongest 'monster' around, and the PC's have proven their worth.
3) Monsters have allies with their own agenda. This could be for example underlings whose primary goal is to supplant the current leader. They might be initially unfriendly to the PC's, but can be won over by parlay - or might seek to parlay if the combat goes against them.
4) Monsters have other prisoners. These prisoners can have their own agenda, from also wanting to rescue the princess, to being doppelgangers or werewolves with a penchant for subtle murder.
5) There is something else down here. Other than the main faction in the dungeon, there can be factions that are tolerated, feared, or venerated by the main faction, but which aren't exactly allies of them. Fey creatures, nature spirits, and even ghosts can survive in the dungeon from some time prior to it being taken over by its current inhabitants. The current inhabitants may concede part of the dungeon to these older inhabitants, and even view them as an oracle or a small god of some sort. These creatures may be overtly hostile to neither party, but form a side of their own with its own agenda.
6) This dungeon isn't big enough for the two of us. The dungeon could have been conquered from something that now exists on the margins of the dungeon ecology, and would like their home back. For example, a tribe of kobolds could be reduced to scavenging from a small set of tunnels on the edge of the dungeon, having been driven out by the bugbears that now make their lair here. In a mega-dungeon, tribe of dark creepers may want their hunting ground back, after having been driven out by duergar miners.
7) Vocalize your villains. Intelligent foes should give war cries, make threatening boasts, call down curses on the PC's, and even banter with them in the midst of combat.