I just finished running this section a few weeks ago.
First, it helps if you read the whole entry. Also, remember that the entries cannot cover every possible contingency; this section is too dynamic. The description of room 20 reads (p. 75):
A lizardfolk shaman is leading two disciples (lizardfolk) in a short
prayer to Semuanya.
If the party arrives here accompanied by friendly lizardfolk, the
shaman initially urges the guards to attack. A successful DC 15
Charisma (Persuasion) check by a character prevents a fight, and
instead the lizardfolk take the characters in custody and take them to
meet the queen.
Next, consider that here are many ways the characters can reach this area, including ways that do not involve meeting the queen. They could even fight their way here. If the party comes in through the correct entrance and someone in the party speaks Draconic, and they think up a good story, they can enter the village normally (read communications and disposition), so there are several ways the can interact with lizardfolk without having talked to the queen.
Also, consider that lizardfolk are not psychic; it is entirely possible for the party to have spoke to the queen and yet for many lizardfolk to not know that. Even if they have met the queen, there is no reason to believe shamans were present.
Next, remember from the entry at the beginning of the chapter on politics among the lizardfolk (p. 62; emphasis mine):
Opposing that group (mostly covertly, for the rule of the queen
remains absolute) are the traditionalists, led by the shamans. The
shamans believe that allying and intermingling with other races is
contrary to the divine will of their god, Semuanya, and that no good
can come of it. Consequently, the shamans hate and distrust the
minister, Sauriv, whom they consider to be the prime instigator of
these efforts that go against nature. They dare not move openly
against him, however, since he enjoys the trust and favor of the
Also, notice that in the "Goodwill Tour" section (p. 63), the Persuasion check DC for earning the shamans' trust is higher than for earning the trust of any other group or individual in the lizardfolk lair.
From this, we can conclude that the shamans want to start a fight or at least an incident. They don't want the party in the village. They see the very presence of the party as an affront to their religion; they dislike lizardfolk who even cooperate with humans. So even if the party arrives with friendly lizardfolk, the shaman tries to create an incident, knowing that if the party harms any lizardfolk it will help sway the queen against them. The shaman wants to start trouble, and the party has to act to convince the guards not to fight. Remember that the guards will not speak Common.
Personally, I love this part because you can use it to show the party how they can easily be tricked into undermining their own goals, if they just react to everything in a knee-jerk way.
Remember, the entries cannot cover every possible contingency. The village is meant to be a dynamic place with dispositions being changed by the players - which is why politics and communications is discussed first. Covering every contingency would fill a book just for this one single chapter. If the entry does not fit based on what has already occurred, ignore it, but chances are if the party is in that spot, it is a ploy by the shamans that could work.