i'd guess two swarms. i would have done as you did. virgin queens tend to be runny. did she seem pretty small? i'd check the one that you didn't see the queen in, tomorrow. most of the time i leave a swarm alone, but if this was one swarm that broke apart, you'll want to get them back together.
sometimes if i find one clump below another, it's because part of the swarm broke loose and fell. it just reformed on a lower branch. at any rate, unless you can spot two queens as you hive them, you'll need to recheck.