So I came across the kanji 凸 today and wanted to know how you write it. When I clicked on the dictionary and watched how to write it I thought to myself that it could not possibly be right. I went to Jisho.org to see and low and behold there was a different stroke order. Not knowing what to do I went to the net to find out more. It turns out both are correct but used at different times. Here is a link to what I found.
I haven't noticed any such kanji, since I don't cross-check them against other sources.
However, Wikipedia (https://ja.wikipedia.org/wiki/%E7%AD%86%E9%A0%86) seems to suggest that the only official source of stroke orders is 筆順指導の手びき, which only includes 881 kanji (the then 教育 ones).
It states that there are several kanji with more than two widely used stroke orders and that the order taught may differ between teachers. Since I don't have the book myself, I can't verify it, but it seems plausible then that there are quite a few kanji like this.
