What likely happened was an inexperienced tech who've misinterpreted a faint line on the Immunoassay as a "fail" and sent it off to the GC/MS. When that happens, the sample would come back as a negative. A faint line still counts as a line, which translates a negative - sample being below the 50ng threshold.

Its a common misconception that the GC/MS is a more "stricter" , or "sensitive" test than the I/A. Its not so. The GC/MS is just more accurate. In actuality, a 50ng I/A screen is equivalent to the 15ng GC/MS. Their cutoff thresholds are numerically different because the I/A screen recognizes the composition of all 31 THC metabolite concentrations, while the GC/MS recognizes only one, which is the most prevalent metabolite concentration (THC-COOH).
To test negative on the I/A, the whole composite of the 31 metab concentrations must register below 50ng.
To test negative on the GC/MS, only that one metabolite concentration must register below 15ng