There are many opinion-based answers possible for this question. For example, in your setting, kobolds and gnolls could have an ancient treaty of cooperation, or ogres could make a habit of capturing and keeping kobold slaves. But there are also mechanical approaches you could use.
The Monster Manual has an Organization line in monster entries. Many monsters have other monsters listed there - for example, kobolds frequently appear alongside dire weasels when they are encountered in large groups. Similarly, gnolls partner up with hyenas and trolls in their organizations. Mind flayers are listed with grimlocks (whom they charm using magic).
Mounts and pets
Humans of antiquity domesticated wolves and horses because wolves and horses hung out in the same places we hang out. If your kobolds hang out around giant badger warrens, they could use Handle Animal to rear and train them as mounts instead of dire weasels. That way, it totally makes sense when they're encountered together.
Slaves and thralls
Many powerful monsters have abilities that allow them to enslave others. Vampires can sire spawn or dominate other creatures to do their bidding. A weak first level goblin sorcerer could use charm person to get an orc chieftain to take him into the tribe. There are all kinds of ways that one creature can magically compel one of a different kind to serve it.
Monsters that work well together
The monsters your PCs are murdering have probably lived in the area for a while, long enough to understand each other's skills. As such, they could have formed symbiotic relationships. For example, monsters such as blues are physically frail but powerful at range. If they live nearby a tribe of ogres and enjoy peaceful relations, the blues could hire ogre bodyguards to guard against threats that like to get up close and personal. When your PCs encounter this combo, it leads to an engaging encounter where two creatures compensate for each other's weaknesses.