I noticed the <kbd>d</kbd> key deleting a line on a single press as well. I am using Spacemacs [email protected] on the develop branch. I do not know if this is your case, but I had an incomplete search in progress.

Steps to reproduce:

 1. In command mode, initiate a search by pressing the <kbd>/</kbd> key 
 2. With the mouse, click on any text in your buffer
 3. Press the <kbd>d</kbd> key a single time and a line will be deleted 

Steps to resolve:

 1. With the mouse, click on your incomplete search  
 2. Either cancel the search by pressing the <kbd>DEL</kbd> key until the search is cleared OR complete the search by pressing the <kbd>RET</kbd> key
 3. The behavior of the <kbd>d</kbd> key should return to normal (at least it did for me)