That highly depends on the species. For example with some ant species that have multiple queens in one hive it can definitely happen that one queen decides to move around. The question is how long will the workers allow her to do that ;)
I noticed that too and indeed it felt quite hurtful for the immersion. But I understand also that it would be hard to keep the map balanced with fight of the neutral species. Just an idea for future levels, maybe the problem could be solved by setting a fixed amount of neutral enemies (dependend...