In evidence, LU said: "There is reasonable apprehension on the part of London Underground that the claimant is being put up by English Heritage, or some officers of English Heritage, who can use the court procedure at public expense."
Martin O'Rourke, regeneration adviser at EH, denied the claim.
He said: "EH does not accept that we are putting up a front. We are seeking an unqualified withdrawal from LUL of these assertions."
In his observations, Justice Collins echoed EH's concerns. He said: "I thoroughly deprecate the assertions made against EH. Such allegations do nothing to advance the defendant's case."
It is thought the judicial review will take place in November, potentially delaying work at the 4.2 ha site.
EH published a report this week by planning consultant Urban Initiatives that backed its preferred solution of building the line on top of the railway arches.
Local community groups have voiced their dissatisfaction with Railtrack's plan for commercial development to go hand-in-hand with the construction of the line.
Not-for-profit developer The Environment Trust unveiled its own vision for the site on Wednesday.
Its architects, HTA and B.consultants, want to build 400 homes and 200,000 ft2 of work space at the site.
They also propose a "wall of water" that would clean trains as they pass through the area.