Strange Growth at Base of Stem

I have two month old plants, and a week ago I added new dirt to the top of what was in the pot, putting the dirt about two inches below where the cotyledon would be (they've already been cut off). Today I noticed small nubs growing at the base of the stem, from the dirt to about an inch and a half up. Also, there's a an actual growth, just above the dirt. Could this be the beginning of a new root, or should I be concerned?

Just looks like its popping another root, nothing to worry about

Ur fine kiddo no worries there

Thanks, folk. There are some nubs down near that growth, above the dirt, I assume those aren't a big deal either?

Why remove or cut off a cotyledon leaf ...?

I've read in multiple guides and forums that you should cut off leaves that are just going to suck up the nutes, leaves that aren't going to produce anything. Was I wrong to do this?

As the leaves start to go yellow the plant is sucking nitrogen and probably other elements, but most visually nitrogen as the leaves turn yellow. To in turn essentially feed off itself consuming energy for other parts of the plant.

Yeah, I had a bit of a gnat problem at first, and went through the drying out of the dirt phase, and the cotyledon leaves turned yellow and were getting crispy. I removed them because they were going to come off on their own if I didn't.