Chances are that there is another reason for the brown spots on your plants.
Are you using plants that are viable in the PH and temperature of your aquarium?
What about the lighting? Are you using the right lighting for your plants?
Maybe there are not enough nitrates in your water to furnish the nutrition your plants need or it could be your plants are competing for CO2. Do you have either very large or a lot of plants? Do you do very frequent water changes?
Are you adding plant foods? These are not necessary with the Eco-Complete substrate, and you may be burning your plants with too much food (?)
I have used the Eco-Complete substrate for years without any problems.
You may use it by itself; however, I add an inch of medium-fine gravel (cap) on top of the substrate at the time I set-up my aquarium..
IMPORTANT: If you want to add gravel to an already cycled tank, you must mix in or "cap" with a little gravel at a time or you may kill your fish, this goes for Eco-Complete or any other aquarium substrates, including plain aquarium gravel.