I think the problem is that there is no end-of-line character at the end of the last line in those text files. I think 'wc -l' merely counts the number of new-line characters in the file.
I.e. it's nothing to do with the # character.

If you don't understand what I mean, look at the contents of those files using something like 'hexdump'.
You can usually configure your editor to always have a new-line at the end of a text file (that you create with that editor) - this is a good idea.