Hey OP, I don’t think it was the rock, or the leaves from the plants.
I think your tank hasn’t had a chance to cycle, and you’re just now seeing the nitrite spike that naturally occurs when starting a tank. It looks like you started about 6 weeks ago, and switched from a 10 to 20gal in the process. It took 2 of my 10 gallons about 10 weeks to see the nitrites show up, and eventually stop rising as the second type of nitrifying bacteria grows to eat the nitrite and pass nitrates as waste.
Just keep on top of small water changes every other day and testing every day. It’s a long process, and so many of us get impatient and add fish before the tanks are cycled and stable. It’s not the end of the world, but it is a little more work than just feeding your fish once a day.
With a well established tank, a nitrite spike should not be a thing. Happy if someone wishes to correct me, but sounds like something happened and the the nitrite to nitrate part of your biofilter changed.
Ok_Week_1601 
How high did you nitrites get?
A nitrites spike usually happens after a rise in the ammonia. How long have your tetras been dead before you removed them?
As far as I know rocks don’t affect nitrites. They’re inert.
Hey OP, I don’t think it was the rock, or the leaves from the plants.
I think your tank hasn’t had a chance to cycle, and you’re just now seeing the nitrite spike that naturally occurs when starting a tank. It looks like you started about 6 weeks ago, and switched from a 10 to 20gal in the process. It took 2 of my 10 gallons about 10 weeks to see the nitrites show up, and eventually stop rising as the second type of nitrifying bacteria grows to eat the nitrite and pass nitrates as waste.
Just keep on top of small water changes every other day and testing every day. It’s a long process, and so many of us get impatient and add fish before the tanks are cycled and stable. It’s not the end of the world, but it is a little more work than just feeding your fish once a day.
With a well established tank, a nitrite spike should not be a thing. Happy if someone wishes to correct me, but sounds like something happened and the the nitrite to nitrate part of your biofilter changed.