Custom Saplings Being wierd

I've seen other people have this problem but the solutions I've seen don't appear to work.
I've made it so that when the saplings grow it will place a structure/schematic my problem is that when it generates the air blocks also get placed which breaks nearby blocks. How do I fix this? Also, the saplings also break bedrock, and just about anything else when placed. is there any way to stop schematics from replacing some types of blocks?