My organization is looking for an alternative way to fix inventory and square things up with our customers when our warehouses mis-ship the wrong product, short ship, or over ship. Our warehouses have their own warehouse management systems so we first have them cycle count and fix on their end then we create the SOs, IFs, and INs to match what actually happened as well as RAs, IRs, and CMs to add product back that did not ship or to bring back the incorrect product that did ship. We are thinking of going to just IAs and stand alone INs and CMs. Any advice or suggestions on how others handle mis-ships, short ships, or over ships both from an inventory and general ledger stand point?

Sounds like you should address operational issues to me, not system issues. It makes sense to create an IF from what you were told shipped, and create RA/CM for those things not actually shipped. You should also consider getting the 3PL on Netsuite and off their random warehouse management systems. Creating IA's for things that shipped is going to look really bad long term. That's like lets just create Journal Entries for everything instead of making any other kind of transaction. The ERP is not only to help you operate, but to give historical data/reporting on what has happened.

Thanks for the feedback Sandii, we do work with our warehouses from an operational stand point to reduce these errors, and I completely see your point about IA's not showing what happened. I was hoping someone might have a process that was less steps and still created the necessary transparency.

I've had a lot of 3PL's in the past and both have major issues (trying to get them to use NS and trying to replicate what they did in NS). It's definitely a tough bridge to cross, as derek tagged above, someone like RF-Smart would have lots of strategies to try to overcome this (obviously at some cost).