There are two possible results to the biopsy: Positive and inconclusive. There is no "negative" for at least a couple of reasons.
The biopsy takes a tissue sample. It does not test every bit of tissue in the intestine. Although multiple samples may be taken, the fact that none of the samples show damage may simply mean that the samples missed it. Go into your front yard, and dig up ten samples, each one square inch. Examine each one for dog excrement. If you don't find any in the samples, it does not mean that your entire yard is free of you-know-what.
Depending on the stage of the disease, and the amount of gluten that was consumed in the period prior to the biopsy, there may be no detectable damage. If you have been truly gluten-free for three months prior to the biopsy, then is likely that any damage that was there has healed. If the progession is early enough, it is also possible that detectable damage is not yet present.
Lab error is always possible, but the above causes are more likely.