When doing function propagation in OMA, we try to limit the taxonomic range to which we propagate functional annotations. This is done by checking in which clades existing function annotations occur. Now, if you did not export at least some genomes from OMA (with the export functionality in http://omabrowser.org/export ), OMA doesn't know to which taxonomic range the genomes belong as there is no clade annotations in any genome. Otherwise, the clade is set to the closest genome for which a clade is annotated based on the (estimated) species tree.
Because there is also no existing functional annotations in a case where the export functionality has not been used, there is anyways no function to be propagated. Thus, putting a warning there might be a bit too strong.