What is the correct way to test for microbials?

I have had the unfortunate situation of cleaning up the messes of two Food Safety Officers that came before me for a Tree Fruit Packing plant. This is my first official role as a FSO, though I have experience in Cannabis cultivation as a Head of House Lead making sure cleanliness and proper PPE were followed. I had suspicions that the Microbial test I had to do on Saturday would come back with Presumptive Positives and started to revamp our current sanitation standards. Sadly my predictions were correct. Though luckily most of said positives were on non-contact locations. 

My current question is that I was told I did the test "incorrectly" being that I tested a few minutes after the sanitation crew finished up, making sure our sanitizer had time to dry, but didn't bring the cleaner and sanitizer to clean the 10" by 10" testing zone to clean that specific zone. I personally feel like this is a perfect way to get a false negative that could lead to recalls or even legal actions because of gross negligence. 

Am I on the right train of thought here? Or is it industry standard to do microbial testing in this way.

Thanks for your advice,

Seathalos

Sounds like you did it right to me.  You want to test the surfaces to reflect your current cleaning practices, verifying they are doing the job you intended.  There is absolutely zero value in testing a site after an extra cleaning that doesn't reflect your day to day operations.