I agree that it shouldn't do that. But other email clients play fast and loose with the relevant standards, leaving Thunderbird unable to distinguish between quoted text, markup and new text that really does need spell checking.

Email generated by M$ clients is particularly prone to this. When I find my reply spellchecking is reporting terms like "panose" and the names of assorted fonts that often aren't even installed, I usually stop, copy the original message text and use "paste without formatting" to sanitise it, replacing all the horrible mso coding that confuses Thunderbird.