When using fix deposit, are dangerous builds the norm due to adding atoms to the simulation? Or do I need to adjust my input to prevent those?
No.
Difficult to say. “Dangeouse builds” is one of the items that may or may not be an indication of a problem. Whether it is, requires a close look at the details and some experimentation. So that makes it difficult to discuss within the setting of a public forum.
We changed the default settings for neighbor list builds in LAMMPS to be a bit more conservative only very recently. If you are using an older version of LAMMPS you may want to try running with neigh_modify delay 0 every 1 check yes as the most conservative setting.