Indeed at the moment, the way to remove an entry or protocol from a collection is to use the popover with the collection icon above the entry content, as in the screenshot below.
There is however a bug in Findings 2.0 (build 5207) where that should also be doable using the backward-delete key. I plan to fix that in a future update soon.
I am also adding in my todo list the ability to use the option key while dragging to move instead of add to a collection (so that it’s removed from the current collection if one is selected). I am not sure when I’ll be able to add that, but I’ll keep you posted here