Negative margins have been known to cause problems in IE7 and below with content being cut off. And, as alias suggests, it could also indicate a problem with the rest of the design. But I think it is wrong to say that negative margins are 'bad development' in all cases. But as always, test test test.
For margins/padding in layouts, I'm with both alias and penders - I try to avoid it if possible as it usually means something is not right somewhere else, but negative values are extremely helpful in background positioning and absolutely positioned items.
It's also useful for anchors that are only images, but you want to have SE - digestible text in the anchor link:
<p id="facebook"><a href="https://www.facebook.com">See us on Facebook</a></p>
I think the best response depends on context: Just because you "may" do something because it valid according to the recommendations doesn't mean you "should" write your code that way.
That's well-illustrated by the examples: a negative text-indent is widely supported as a technique to improve accessibility. Using it to load search-engine bait is black-hat SEO that will be penalised by search engines.
Negative off-sets (margin and position) have any number of useful applications. But we've all cringed at such (badly) over-engineered documents that the natural layout has been destroyed to point every single element has to be manually dragged back into the view-port because the content has been sent (as Lucy says so well) "into another universe".
As this is in the context of a cms jelly46, I'd ask the question at two levels.
Why are you using a negative to re-position elements? (If to achieve a legitimate outcome fine, but to "undo" issues caused by the basic styling of the document, probably not).
If you are using negatives to "undo" the styles imposed on you by the cms/don't have the autonomy to code as you choose: Should you be using that cms? (Client specifications make not give you freedom to change the cms, but if you do, having to "undo" the cms suggests that particular cms isn't the right tool for that particular job.)