The silicone is not what makes it waterproof, the gasket does.
The reason to put silicone on the gaskets is to lubricate them, that's all, it does nothing towards making anything waterproof.
I see many movements damaged from members thinking the more silicone they jam into the crown and tube or the caseback the more waterproof the watch will be.
The silicone should only be rubbed on the rings, it should look "wet" if you see chunks or blobs of silicone, you have way too much applied...
Silicone is next to impossible to remove, and will destroy the watch cleaning fluid, so use with caution.
To make the pushers waterproof, disassemble them (by removing the screw or C clip), then inspect and replace if needed the orings, rub a light coating of silicone on the o'ring, and re-assemble and test, there isn't much more you can do.