I using Github Atom in Windows, but I met this problem (https://github.com/atom/atom-shell/pull/452).
Luckly, I see atom-shell v0.14.0 fixed this problem. But later, the Atom v0.117.0 was released, it still using atom-shell v0.14.0. That means, in windows, we must confirm move to trash by Atom, and must confirm again by explorer. BTW, confirm dialog from explorer haven’t icon in taskbar.
PS: atom-shell v0.14.0 was released in Jul 21, 2014, 10:23 PM CST, Atom v0.117.0 was released in Jul 23, 2014, 3:42 AM CST.
Please update the Atom’s atom-shell. Thank you very much!