On the wiki it's stated pretty clearly that using large amounts of units in the modules, but limiting them dramatically in the active limiter is not the ideal method and can cause issues. I'd personally try raising the amount with the limiter like Incontinenetia said and then lower the civ/mil obj spawns if needed for balancing.

Making a mission with a lot of Virtual AI then artificially spawn-limiting them is inefficient and may get weird results, such as units spawning in behind players and moving into areas already cleared. Best practice is to reduce the density or number of Virtual Profiles in the Placement Modules to improve performance.