There are sofrim, including well meaning ones, who sometimes appear to be ignorant of some of the basic halachos of writing STA"M. Even here in this forum, without mentioning any specific cases, I occasionally notice posts or comments that indicate the author's ignorance of very basic halachos.
I am not sure exactly what the source of the problem is, but I think the solution is simply that sofrim need to learn the Kesses Hasofer (including the Lishkas Hasofer, of course), and review it again and again.
Additionally, I think that in many cases, learning other seforim on writing STA"M may take away from the knowledge of the halachos, as people seem to get confused or distracted from the basic halachos as brought down in the Kesses Hasofer. I also think that it is unnecessary to additionally learn the Mishna Berura (Mishnas Sofrim, etc.) on writing STA"M, and I am unsure as to why that is a requirement by some who grant kisvei kabbalah (even though I do think it's a good idea to learn that once proficient in the Kesses Hasofer).
I have discussed this with some very respected sofrim who were in agreement with me in that the Kesses Hasofer (including the Lishkas Hasofer, of course) is ALL that is necessary to learn in order to be a proper sofer, and that often learning other seforim on writing STA"M distracts from focusing on the knowledge in the Kesses Hasofer.
I hope no one takes this the wrong way, as I mean this only constructively. (Also this post is intended for Ashkenazi Sofrim who hold by the Kesses Hasofer, and not meant to CH"V belittle any other mesorah.)
My main point in this post is that sofrim, no matter how experienced, need to study the Kesses Hasofer again and again and again!
The Kesses Hasofer can be downloaded or read for free here (in an old print): http://www.hebrewbooks.org/8308
It can also be purchased in a new and beautifully clear print here: http://zbermanbooks.com/product-64947.html