Edited my comment with the version number.

Factorio version 0.12.29

Also, put the report on GitHub.

I noticed that the version was pre-released. Reverted back to the previous release, and don't have issues now.

Treefarm-Lite__/control.lua:573: LuaEntity API call when LuaEntity was invalid. CTD Three farms producing with germlings. It looks like possibly that it is happening when trees are going from medium to large. Treefarm Lite Version 0.3.4 Factorio version 0.12.29 Mods: Advanced Logistics Autofill Bob'...