Hi

To remove auto allocation on sales order you can follow the following steps

1. go to Parameter values "All>Setup>General parameters" .

2. under VEN - Sales on folder level or Company level Select SAL in Details.

3. Change INIALLORD and RSTALLORD to 'No'

TO REMOVE SHORTAGE

4. Go to Inventory STO and select MIS miscellaneous Details

5. Change the GENSHT to 'NO'

Hope this Resolves your Issue.

I still want to create shortages, and the ability to auto allocate, but I do not want it to auto allocate when I press the save button. 

Can you please share the screenshot of the screen for clear understanding, where exactly you are pressing the save button

I am pressing the save button on the sales order screen. (GESSOH) On the sales order screen, when we have an order and it is partially allocated, we would create a shortage. When we press the save button after allocating partially, and creating the shortage, the system is like hey they said this is short but I see products available to be allocated so I am just going to allocate the remaining products to this order even though the user did not allocate the product himself. 

I am pressing the save button on the sales order screen. (GESSOH) On the sales order screen, when we have an order and it is partially allocated, we would create a shortage. When we press the save button after allocating partially, and creating the shortage, the system is like hey they said this is short but I see products available to be allocated so I am just going to allocate the remaining products to this order even though the user did not allocate the product himself. 

You can refer this link..

https://www.greytrix.com/blogs/sagex3/2015/09/02/how-to-disable-inventory-shortage-generation-in-transactions-and-inquiries/

it is already set to no