Nothing major, beyond the controversies listed here[0] and the developer's more cavalier approach to whitelisting. Plus resource usage was double what was on offer by the much more fine-grained uMatrix. At the time at least. Maybe still.
The Tor project still bundle NS in with their browser, hardened, I believe (stricter whitelisting, for one) but they clearly still trust it. Better than nothing, but far from perfect IMO.
As far as I know, there was a single incident where a version of NoScript put its own site on the user's AdBlock Plus whitelist. Other than that, NoScript has not done anything shady and continues to provide features that have no equivalent in any other browser or extension.
