Using the reply editor in WYSIWYG mode
is prone to dropping a lot of Road Apples

of extra tags. That's why I never use it in that mode. It also does not seem to cleanly cycle between WYSIWYG and non-WYSIWYG mode (they're not perfectly reversible). The developers have been discussing this behavior lately, and say that they have some code fixes, but those won't be available until SMF 2.0.3 at the earliest.
Pasting in text from elsewhere is not WYSIWYG, so please make sure you have your terminology correct. Any editor can do that. WYSIWYG is defined as, say, pressing the "italic" button and then text is italicized
as you type it. Non-WYSIWYG would be typing in the text with manually-entered "i" tags, or highlighting it and pressing the "italic" button to add "i" tags, but you don't see italics until you ask for a Preview.
Now, if the text comes over with various
control codes embedded in it, there's no telling what will happen on the SMF end, especially if the editor
is in WYSIWYG mode. I don't think SMF's editor behavior is well defined for embedded control codes, and every word processor is going to have its own. If you're bringing over text from a web page, maybe it's bringing with it HTML tags (although I think they're
not supposed to be picked up), and it's getting confused over whether there are "ending" tags or not.
My preference is to stay out of WYSIWYG mode, as it does more harm than good, and just frequently Preview the post to see how it looks. You want to make a habit anyway of Previewing before Posting/Submitting, just to catch any glitches and see how the final formatting looks, something which the WYSIWYG mode doesn't always seem to do quite right.