I like to load directly from the mining depot into train, but the train tracks usually go over the ore, and when they come into the station they usually end up killing a drone or two each time. So I was wondering if there was a way to mark certain tiles to be ignored?

nope

:( alright I'll make do

So I was wondering if there was a way to mark certain tiles to be ignored?

nope

but in some other discussion thread at https://mods.factorio.com/mod/Mining_Drones/discussion/5e6b4c42d705fb000e6ab343
Klonan at least said this :

You can set up a safe rail crossing if you want, they will open gates
But if you're not careful, the trains will squash them

it will be a nice challenge to build that. you only need to watch that you don't build rails on top of any ore.