When you unload from vehicles/ammo boxes to the arsenal, you then have to go into the arsenal and click the "To Crate" Button.
The AI will automatically select from equipment in your arsenal when they spawn.
If you can replicate your issue with the arsenal, please join our discord so we can have a look at your .rpt log. This will help us in pinpointing the issue.

OK thanks for the response. My problem is I am unable to access the arsenal most of the time as it just loads for ages with nothing happening for some reason. when I was able to access the arsenal it was empty but everything I have collected is in the inventory. My understanding is I need to go into the arsenal and then click to crate? I'm fine with using the inventory instead but wondering how my AI start using the better weapons I have collected if none are transfering to the arsenal. Ill try again now with your method I have just never had trouble with the arsenal before on antistasi.

Thanks I now know how to transfer the weapons into the arsenal but for some reason half the time I try to use the arsenal it just keeps loading and I'm forced to quit as it doesn't do anything. Any ideas what might be causing this? Thanks again Meerkat for explaining how to transfer the loot!

Try running the scenario through a LAN hosted server as this tends to make the mission a tad more stable.

Thanks seems to be fine using LAN

Pardon my idiocy, but how do i run the scenario through a LAN server?