Hi! Thanks for the bug report!
For the first issue, the correct number of lines are there but the styling in the theme (presumably) you're using is making the line numbers not line up with the actual lines of code.
I tried it out on a different theme as a test and it works fine:
I'll work on fixing it so that the theme you're using doesn't impact the code's styling like it is now. Sorry about that.
However with this newer version of the highlighting script, you can just select and copy the code like you would any other text! You'll no longer get the line numbers included. This makes the view raw source and copy to clipboard buttons redundant and just in the way.