I don't think that flags were ever really intended to be used this way. You flag posts for moderator attention if you think that they need to be disposed of or are otherwise beyond saving. For the most part, these consist of spam as well as questions and comments posted as answers. You should not flag something because you think that it is technically inaccurate: that's what downvotes are for.
I agree that tag wikis are a bit more difficult to deal with because you cannot downvote them if you believe they are inaccurate or low quality. However, you can edit tag wikis (or at least make suggested edits) to improve them and correct any technical inaccuracies that you find.
If, however, you notice a number of empty tag wikis that could use some attention and you aren't knowledgeable enough about the subject material to edit them yourself, you could try asking the community here on Meta.SO to improve them. Be careful, though: you'll probably run into some backlash if you ask a new question on Meta for each and every tag wiki that you want improved. I would suggest finding and prioritizing a handful of tag wikis to include in your post here, if you are so inclined.
msh210 makes a good point that you should only ask the Meta Stack Overflow community for help improving tag wikis on Stack Overflow or Meta Stack Overflow. If you would like to ask for help improving tag wikis on other sites, ask their respective Meta communities.