I just received the answer for my first submitted paper. It was rejected but they annexed the answer of just one referee. Is it normal to reject a paper based on the review of a single referee? Can I use this as an argument to ask for reconsideration? Of course this would not be my single argument, since I found issues with the review itself as well. (It questioned the validaty of my methodology even though I cited a review just about the methodology used.)
It is normal. Often there is one referee who writes an extensive review, whose judgment weight heaviest with the editor. If there are 4 reviews, 3 are in the "publish" half of the spectrum but are brief (not adequately justifying the recommendation), and there is 1 "reject" review which extensively argues against publication, an editor will either have to apply his/her own knowledge of the field and decide which argument carries the day, or will need to request an additional review. Good editors do not just count up the plus and minus values, they have to evaluate the evidence in the reviews.
If you make the case for reconsideration, I think it should focus on the question of whether positive evidence in the reviews has been undervalued. There's not much you can do if the negative reviewer is (unbeknownst to you) The Leading Authority.
In my experience, it is typical for papers to receive either zero reviews (editorial rejection) or multiple reviews (usually 3-4, but occasionally 2 or 5). Having just a single review (accept or reject) is very unusual. One possible explanation is that the editor formatted their editorial rejection as a review; another possible explanation is that you were dealing with a publication venue with a rather slipshod process.
You can email and ask for clarification. It is not, however, likely that you can get the decision changed in any way: if the editor found your paper problematic enough that they willing to reject with a single review, they are unlikely to change their mind on for purposes of "due process." Improve the paper, find a better venue, and move on.
It happens -- at least it's happened to me -- and although I don't know about the etiquette of asking for reconsideration, if you believe the bad review is based on an incorrect reading of the manuscript, then I think it's warranted.
The time this happened to me, I had two very good reviews on a paper and one really bad review. The two good reviews were short because they liked everything in the paper and had nothing else to say. The one bad review was bad because the reviewer was biased against my premise and did not examine the evidence I presented. I contacted the editor and pointed these things out and eventually the paper got published. So, there's not much to lose by touching base with the editor unless in your situation doing so would be a serious faux pas.
It is not so common but it still happens quite often that a paper is rejected by only one referee, especially for smaller conferences. Usually a paper is assigned to a few reviewers. But some reviewers may be busy and may not send their review on time. In that case, the decision may be taken without all reviews.
And generally, it will not work if you ask for reconsideration unless there would be some major error or some very serious reason to do so. Besides, according to my experience, it happens quite often that some reviewers don't understand something in a paper. But most of the time, it is the fault of the author because something in the paper is not clear enough. So if the reviewer did not understand, it may just be an indication that you need to rewrite the paper to make it more clear so that the reviewers will not think about something else. Don't forget that reviewers are not always expert on your topic.