Hi @Memphis118,
welcome to SKFA.
It does not look like you have run into a problem with your tank. The tank looks cycled and should be ready to be home to new shrimp.
However, if you ever use Bacter AE ,or any other bacteria in a bottle product, be aware that these bacteria need oxygen to survive and grow. That is, they are aerobic. So by placing them under the substrate, they are starved of oxygen and won't grow to optimum. Probably why you have heard people say it will rot.
When you add more Bacter AE, just dissolve it in your change water and pour it into the water column next time.
Just remember, if you ever start a new tank in the future ... minerals go in the bottom of the tank, then substrate on top. Bacteria additives you buy in a bottle needs to go on top of the substrate, or at least in the top 1cm of the substrate where it will get the most oxygen.
If your tank is still relatively empty of ornaments, plants and shrimp, you could give the substrate a stir to promote more oxygen to the lower levels of the substrate. Otherwise, just leave it as is and add your shrimp.
Good luck with the CRS.