Hello,
On my Minecraft server, which has only ExNihiloCreatio, writes:

[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Oak Sapling with meta 0 already exists, skipping.
[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Spruce Sapling with meta 1 already exists, skipping.
[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Birch Sapling with meta 2 already exists, skipping.
[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Jungle Sapling with meta 3 already exists, skipping.
[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Acacia Sapling with meta 4 already exists, skipping.
[17:17:54] [Server thread/WARN] [Ex Nihilo Creatio]: Crucible entry for Dark Oak Sapling with meta 5 already exists, skipping.

The Version Minecraft - 1.12.2
Forge - 1.12.2-14.23.3.2655
Mod version - 1.12-0.2.2

Full log - https://pastebin.com/UG6LmmCu

That warning doesn't affect anything. Probably caused by this function registering both the oredict treeSapling and each individual minecraft sapling.

I don't have time right now to debug, but I'm inclined to say won'tfix, because vanilla oredicts aren't always reliable to exist—other mods could mess with it—(so we want to register the vanilla saplings) and the oredict provides fairly good crossmod support (so we want the oredict).

Thanks a lot.