Pen three on the Leppings Lane terrace had an estimated 1,296 fans inside when the safe capacity was just 678, the jury was told.
Structural engineer John Cutlack, a stadium expert, told the inquest photos had been used to estimate the number of fans inside that pen on April 15, 1989, before Liverpool's FA Cup semi-final against Nottingham Forest at Hillsborough Stadium.
Ninety-six Liverpool fans were crushed to death in pens three and four.
Mr Cutlack has been instructed by the coroner, Lord Justice Goldring, to give his expert opinion. Mr Cutlack said he estimated the actual correct safe capacity for the whole Leppings Lane terrace to be 5,426.
But when the ground was first designated as needing a safety certificate in 1979, the total capacity for the Leppings Lane terrace in the certificate was given as 7,200.
Christina Lambert QC, counsel for the inquests, asked the witness: "Those were effectively 50 per cent more than the safe capacity of those pens? That's before you add in an influx over that capacity?"
Mr Cutlack replied: "Yes."
He said some of the "seeds of the disaster were sown in 1979" when the capacities were estimated higher than he believed were safe.
The hearing, in Warrington, continues.