minecraft bottles and potions cant go into the petal apothicary even if you make a recipe with them.

Buckets (or other fluid-capable items) can be dropped "into" Apothecary to fill it. So that the Apothecary doesn't eat these items when they're done, all fluid-containers are blacklisted from the Apothecary. (See vazkii.botania.common.block.tile.TileAltar#collideEntityItem.) Bottles and potions count as fluid containers.

Possible workaround: After fluid-cap check, reject item only if the item cannot be filled with 1000mb of water

This issue is stale because it has been open for a while with no activity. Remove stale label or comment or this will be closed soon.