It's pretty clear to me. This is all about the ridiculous, mendacious and downright unlawful way in which Mignini prevented Sollecito (and Knox, for that matter) from getting access to a lawyer in the three days following their arrest and detention on 6th November.
Basically, there's an allowance in the Code for PMs to deny arrested persons access to counsel - but ONLY under extremely unusual and strictly-defined circumstances. In essence, the PM has to have reasonable grounds to suspect that to allow access to counsel might have a significant change of hampering the investigation and/or perverting the course of justice. And pretty much the only time this is at issue is with serious organised crime (e.g. the Mafia) or terrorism. In either instance, lawyers might wittingly or unwittingly be used to convey information such as alibis, or to intimidate potential witnesses, or to hide/destroy evidence.
If a PM wishes to invoke this denial of counsel, (s)he must set out the written grounds to do so, and present them in writing to the arraignment judge. The written grounds must specifically argue that the circumstances are extreme and unusual, and must spell out the reasons why the PM feels that the investigation might be hampered and/or justice perverted if the defendant(s) were to get access to a lawyer.
Mignini simply invoked this denail on a whim. Because it made things easier for him, and probably because he thought that Sollecito and/or Knox might further "buckle" without any legal advice, and might totally "spill the beans". But what he did was unlawful and unfair. And what's more, the supine arraignment judge, Micheli, blithely waved through Mignini's invocation of the denial of counsel - he actually asked Mignini if he (Mignini) had completed the formal written motivation, and Mignini demurred (he hadn't written any such thing....). So in a sense, Micheli is as guilty as Mignini on this matter. It also further illustrates vividly just how improper and unjust is the cosy relationship between judges and PMs.
And as I read it, Mignini has basically been formally told off by his superiors. It will sully his record, and presumably it will also potentially have some bearing on the rest of his career. The man's a disgrace for many reasons. This is just one of those reasons.