Namely that a traffic light system is a huge, huge, HUGE oversimplification of complex issues. While the analysis seems fairly transparent, I don't think many people will actually look into it past the traffic light.
I checked out the uni I went to: apparently the students union got an amber light because of "no tolerance to sexual harassment". How exactly does that violate free speech? The right to free speech unequivocally does not give you the right to harass people in any way. Similarly "Rules and Regulations for the Use of Information and Communications Technology" is an amber for institutions: does that mean all AUPs are in violation of freedom of speech? Most of them come down to "please don't hack our infrastructure or download anything that will make the police come round".
Also when things like "bans on specific ideologies" are very likely to get misconstrued. Banning groups which verbally harass others is likely going to be seen as a ban on free speech, despite the fact that such bans may be warranted.
The whole analysis and ranking system seems biased, and completely garbage to me.
Edit: since I'm an idiot and didn't realise that you could expand the amber/red points on the site, my uni SU's "no tolerance to sexual harassment" was due to them adopting the NUS (National Union of Students) guideline that sexual harassment is defined as ‘any unwanted comments which makes someone uncomfortable’, and the ICT rule was ‘Users must ensure that the content and tone of their email messages cannot be considered offensive.’
Both of these appear reasonable to me. There's some genuine debate to be had over the issue of no-platforming but all this site is doing is furthering their own agenda, which seems to be that they should have the right to insult and harass people however they want. As always, this is relevant here: https://xkcd.com/1357/