This is not my original idea. The inspiration I got from +Eric Hoffman at Google+ Mutant Future group. His blogpost "Mutant Future Expanded Wilderness Rules" is where I got the idea from.
When you roll for random encounter, also roll an additional d6. If the d6 shows "6" roll twice from the random encounter table. The encounter will be these two creatures interacting somehow. Also when you had a result 6 roll again - another 6, add an additional creature to the encounter and roll again.
Example: Before I roll d20 to see what the random encounter is, I roll a d6 and have a result "6". So that's two critters they encounter. But because I scored a 6 I roll again. Blah result is 3. With another 6 I'd got to mix one additional creature in the encounter extravaganza!
When you know how many encounters there are, roll their relations to each other:
1 - Aggressive, they most likely fight each other
2 - Suspicious of each other
3 - Passing by
4 - Close to each other, neutral
5 - Friendly, but not associated
6 - They work together
To make things fun, roll for each encouter pair. For example of three encounters Spidergoats and Morlock might be passing by when Spidergoats work with Brain Lashers but Morlocks fight them. Try to figure that out, nah, let player characters do it! You grin and let the mayhem begin!
If you feel that 1 in 6 change for double-encounter-situation is too big, then just rise the die size. Use d12 or d10 instead.