There is every reason to quash the whole case against Flynn. The internal memos, which were recently unsealed, at the request of Flynn's attorney, demonstrate that the FBI agents conspired to set him up. They were talking about how to get him, either convicted, or fired. Perjury traps can be set on anyone, it's not that difficult to fuck someone over when they want to.
I don't think you know what a perjury trap is. A perjury trap as legal defense requires that the questions asked are not material to what is being investigated. While they may have figured he would lie about something and wanted to put him into that position, it is only a problem if they were trying to get him to lie about something unrelated to their investigation. Lying about something material to an investigation is always illegal. He didn't have to lie despite the pressure.
Now... Were FBI agents biased in their treatment of Flynn? I don't know. They definitely deemed him a threat to the country and desired to bring him down. But that isn't a legal problem so long as they follow the law. Being biased against someone, even an innocent someone, is not a defense unless that bias results in a breach of law. Bias is material to a defense of prosecutorial misconduct, but it is not misconduct itself.
Flynn either lied to the FBI and plead guilty or lied in his plea. Unless there is actual misconduct and not bias or simply legal application of pressure, one or the other of what Flynn did is a criminal act.
Separately, I agree with the IG findings that there were some problems at the FBI which deserve attention in order to serve the public best but did not constitute misconduct in this investigation.