You do realize that "things happening without a logical reason" is not the same as not providing an explicit logical explanation for something that may be inferred implicitly from other information. Munsu's statement is consistent with your 'definition'.
There is enough information present in the story to come up with a logical explanation of why Chrollo would believe Pakunoda's mind reading wouldn't work on Hisoka and thus drop it from consideration(even if all of this went on inside his head). In particular, the Spiders have already acknowledged the chain user as an intelligent foe. It would not make sense to assume that your opponent (who you consider smart) would simply overlook Pakunoda's ability if told about it.
Was any of this explicitly laid out for the viewer? No, but that doesn't necessarily mean things happened "without a logical reason". The existence of even a single logical explanation (even if left unstated) that is consistent with the rest of the story prevents it from being a plot hole.