Ok, I think I've got a semi work around to avoid crashing.
Couple things. The OOB doesn't know what to do with mounted companions. If you look at a formation box, you will see the total number of troops in the formation off to the side. Then it will show the number of modifiable troops via the slider. The extra troops in the total off to the side are your companions the OOB doesn't know how to manage. By default, it considers them infantry.
If you try to manipulate these formations with these companions in them, it tends to cause a CTD. It also makes it very difficult to sort your companions out. So, here is how you do it.
First, it sorts mounted companions as infantry, and it prioritizes them by group number. So, let's use an example. You load up a battle, and your Infantry slider shows 30/30, but the total number of troops in the formation reads as 40. You have 10 unassignable companions in that formation. If you attempt to use the slider here it will likely CTD. Make another infantry group that is empty. If the group they are currently in, is say, group 5, make the new group, group 1, 2, 3, or 4. Now, delete group 5. Your companions will resort to the highest avaliable infantry group. Now, make another infantry group with a lower number priority, so 5, 6+ etc. Now you can use the slider to move all the infantry out of group 1. It will leave your companions sorted by themselves in group 1.
If your archers/cav/whatever get messed up like this. Use the same principle, but use the multi unit formation. Inf/Ranged or Cav/Horse Archers. Basically, once you create a new empty formation that corresponds to the one that is stuck, you will be able to use the new formation to pull units out. Remember the lower the number the higher the priority for the companions to bounce to when you delete the formation the companions are stuck in.
Hope this helps anyone having crashing issues.