I'm surprised that they would act that similarly, for the simple reason that each one would have a separate location, which spins off to all sorts of differences. For example pathfinding, sensory differences, etc. Check the simultaneous behaviour isn't a bug, e.g. sharing common variables.
That said, pick a few configurable attributes such as aggressiveness, caution, weapon preferences, sensory sensitivity, etc. Assign (manually or randomly) each agent's attributes somewhere in that range. I don't think any one attribute would need a huge range to get interesting differences.
In practice I would say that it's not a problem because most games rarely have large simultaneous spawns. There may be multiple spawn locations, fixed patrol routes, etc set by the designer.