I am writing a long thesis and suddenly EndNote mixed reference order: it does not start it with the number 1 but instead with 3. And what it count as a number 1 is actually a reference number 11. I saw the post how to solve the problem when one has references under the figures (so the endnote prioritize it) but the fact is that I don’t.
Does someone know how to solve that problem?
Thank you in advance! 
So you are absolutely certain you don’t have text in a box or in a frame with a citation? Unformat and search for that citation to be absolutely sure.
So I realized this in another thread, as it is the textboxes and not the frames that are the problem, and Word 2010 makes it harder to insert a frame – but here are instructions that aren’t too painful.
This is the simplest way to insert a Frame as opposed to a textbox in Word 2010/2013 avoiding the legacy hack.
See https://support.clarivate.com/Endnote/s/article/EndNote-Citation-numbers-out-of-order?language=en_US for a discussion of the likely cause (citation inserted into a textbox usually associated with a figure), but view this recent solution to the problem which is a better fix than that oulined in the first link.