Did you seed your tank with mulm and black beard coated medium?
Test for Ammonia, Nitrates and Nitrides. If you are getting Nitrates, that means the cycle is nearing completion.
If you change or add any of the contributors of ammonia, you effectively detriment homeostasis and a new balance needs to be established. What makes this trickier is doing this in only a 2.5 gallon tank.
Its normal for mulm to break down if transplanted to a new tank so i wouldnt worry too much about that. Is there substrate in the tank or is this barebottom?