I was trying a simple infantry vs infantry with BLU_G_F vs OPF_G_F & came across some bizarre stuff like Blu teams spawning in the OPFOR TAOR & OPFOR hellcats being used for Blu Logistics (causing blu to shoot at their own supplies)
I also tried switching a faction out with IND_G_F but same thing happened.
Could help more if you post more information (screenshots of menus) or upload the mission for others to take a look at.
Edit: Make sure you are using the proper rebel sides as Savage stated below
Make sure your side settings are correct in the editor (ie: resistance friendly to blufor, etc). Double check your faction settings in all placement, CQB and OPCOM modules (make sure they are set to Rebels Red and Rebels Blue and that the proper faction classnames are in the CQB modules.
If that still fails please post your RPT (or server's RPT if this is on dedicated) to pastebin.com and link back here.