To remove specific songs from Crates you've made on the app, just follow the instructions below.
On the app, click the Crates icon at the bottom of the page.
On the Crates page, click the My Crates tab at the top.
From there, click on the Crate you'd like to edit.
On that Crate's page, you'll see an "Edit list" button at the top of the page.
When you click that, red trash can icons will appear next to every track in that Crate. Just click the trash can next to the track(s) you want to remove and it will be deleted from the Crate.