The High Court in Glasgow heard that a 90-page expert report on Miss Spence's phones, and those of the four men accused of murdering her, only made mention of two of her mobiles.
Cell site analyst Dominic Kirsten had told the court that the report was one of the largest ever compiled.
Mr Kirsten was giving evidence at the trial of Colin Coats, 42, David Parker, 38, Paul Smith, 47, and Philip Wade, 42, who deny abducting, torturing and murdering Miss Spence at a flat at Meadowfoot Road, West Kilbride, between April 14 and 28, 2011.
Under cross-examination by defence QC Derek Ogg, representing Coats, Mr Kirsten was told: "We may hear from a witness that in the space of 18 months Lynda Spence had at least 20 mobile phones, but your report deals only with two phones." He replied: "That's correct."
Mr Kirsten was then shown documentation for a pay-as-you-go phone used by Miss Spence from April 2, 2011. The jury was told the phone was disconnected on June 2, 2011.
Mr Kirsten agreed with Mr Ogg that the phone number had not been forensically examined and that it covered "an interesting person and an interesting period of time in the inquiry".
Mr Ogg added: "Your report does not deal at all with this number which was known to be used by Lynda Spence."
Mr Kirsten replied: "That's right."
The QC claimed the report only gave a partial picture.
Mr Kirsten said: "I haven't looked at this number and I don't know what it is."
Miss Spence went missing on April 14, 2011, aged 27. The trial continues.