Biological replicates
Biological replicates involve separate mRNA extractions, followed by separate labellings and separate hybridizations. Still these will typically be carried out by the same investigator, using the same technique, the same set of reagents, perhaps on the same day, etc. Some of this sameness is desirable.
Depending on the source of the mRNA, separate extractions may involve the same cell line or tissue sample, but in many cases, they will involve distinct organisms, e.g. different mice from an inbred strain, or different pools of cells. This introduces extra variability.
The nature of the biological replicates must be related to the target population (an inbred strain of mice, a type of tumor, etc.) at which inferences are aimed.