Hello! I have had this question in the past as well. It is my understanding that the ending count on SAC is suppose to match your actual inventory at that time based on everything you enter. It is a mathematical equation but the results you get should match your actual inventory.
Start inventory + intake - outcome = end count
When I first started paying attention this this I was only off by one or two numbers here and there (what SAC said we should have in inventory was off by one or two animals from what Petpoint says we should have) and was able to find where my errors were with some time. For me, we run a s/n clinic as well and rarely those intake numbers cross over into the shelter inventory, but in some cases they do, and it was what was throwing me off. I was calculating the outcome but not the intake because they originally came in through the s/n clinic but we kept for adoption (as an example.) Also make sure your system software (we use Petpoint) is calculated for the end of the day (time.) At first my numbers were wrong because I was putting in the wrong time of day. Sometimes finding out where I'm off is difficult and time consuming, and we run a smaller shelter, but the numbers should match your actuals.
Hopefully this helps!