Hello,
you have Unit Control mod, the automatic behaviour generally doesn't run ( in v4.5 ) , you must rely totally on Unit Control command features.
If your units are operating automatically, and then you try to use Unit Control, that will break the Unitgroups which are used during squad AI.. It is strange that it is having both options.
Can you use the Robot Army squad selection tool and command the squads that way without it causing a crash?
I am very slowly working on v5.0 of the Robot Army mod, which you can get from github in the "unstable" branch and try that out.
that fully uses the Unit Control mod, but also takes control of units based on which assembler they came from, and you can put a settings module on each assembler rather than a global setting. try it out? https://github.com/kyranf/robotarmyfactorio/archive/Unstable.zip