Why did Congress refuse to seat the delegates elected under Johnson's Reconstruction Plan?

Because the Reconstruction plan he afforded to Southerners while Congress was adjourned was too generous by the Northern Republican's Standards. The Southerners had their property and citizen's right restored without having to make any concessions with regards to African-American's civil rights. The Southern states enacted Black Codes (special provisions to state law that only applied to African Americans). Blacks were not allowed to vote. Also, all their former Confederate enemies in Congress were re-elected into power.