In many text editors, when using the find/replace option, pressing the Enter key cycles through the places in the file where the matches are found. I was thrown off slightly when Atom put me back in editing mode after finding the first match and since I knew the place I was looking for was further down the file, I was hitting Enter several times in quick succession and inadvertently added a bunch of new lines in the middle of my code. This is enough of a habit for me I continue doing it on occasion even when I know now that this will happen.
It is worth considering have the Find/Replace interface in Atom work similarly to other text editors in this way. Overall, great program though! I have really enjoyed using it so far!