There are so many irregularities in this case that it would make a very long list. Here are just a few off the top of my head:
After the (very surprising, if you know Swedish law) verdict, some journalists found out that the judge was biased. He had an extra job where he worked with one of the plaintiff lawyers. And he was member of a copyright-fundamentalist club promoting harsher copyright violation penalties where he regularly met several of the plaintiff lawyers. The judge kept this secret during the trial. A tribunal of three judges was set up to decide if the judge was really biased, but when their names were made public, it was revealed that all three were also biased. The tribunal was replaced with three more judges, and although it was revealed that at least one of the judges in the new panel had connections with one of the plaintiffs in the case, she was not replaced. The new tribunal decided that the judge was not biased.
Just five months before the big raid on The Pirate Bay the chief prosecutor in the case wrote a memo where he concluded that it would not be possible to convict the people behind TPB for copyright violation.
There are heavy rumors and a lot of incidental evidence that the raid against TPB and the resulting court case was done on a direct order by the government. This is illegal in Sweden because it means that the court system could be abused for political purposes. Documents that could tell if this is the case are kept secret by the Swedish government.
The policeman heading the police investigation got a new job immediately after the police investigation was concluded. His new employer was one of the plaintiffs in the case, and he negotiated his salary with his new employer in the final stages of the police investigation.
The legal advisor of The Pirate Bay was arrested during the raid and forced to give a DNA sample. (This is possible in Sweden if the charge can give at least one year of prison time and a DNA sample is relevant for the case.) One of the people later convicted to a year of jail time was also arrested and refused access to a lawyer during initial police questioning. (Possible in Sweden if the charge is is not likely to give jail time. And Swedish law admit evidence even if the police has obtained it illegally.)
Anybody who knows Swedish law and have followed this case closely (ie. read all court documents) know that this case is a joke and a distortion of Swedish law. This is a political court case intended to bend Swedish law so people can be convicted for "crimes" that are not illegal according the the letter of the law.