Creating express entry profile is not the same as applying for PR. You can apply for PR only if CIC invites you to apply. So unless you have got an ITA and submitted application for PR, the answer to that question should be NO.
I am of the same opinion just was a bit unsure. So I will do the following::
Question 1. Have you ever applied to Immigration etc.
Answer Yes because I created EE profile
2. Question Have you ever applied for PR
Answer No
Do you think that this is OK? Should I mention in LOE that I mistakenly answered yes on question "have you ever applied for permanent residence" when filling out new profile?
Honestly, I cannot recall the exact wording of that question which I was asked to answer regarding my previous applications.