Not every unicode character occupies 3 lines, but '⊆', '∈', and other unicode mathematical symbols occupy 3 lines in emacs on my system.
How can I fix this rendering bug?
I'm pretty sure that the answer is: try another font.
There was quite a lot of discussion about this problem recently in the thread for bug #20628 of the Emacs bug list.
You will even see some info about particular fonts there, which might be helpful for your particular question. Oh, and note that there were some changes made to how Emacs picks a font, as an attempt to deal with this problem. These fixes are planned to be merged into the Emacs development trunk soon.