(1) Animal welfare. The researchers are aware of the animal welfare issues at stake, but a collection of metrics around pod culture, stress, and reproduction should be tracked across experiments to make sure we're not hurting the animals. If thresholds are exceeded across multiple experimebts with this tech, the research should stop.
(2) Acoustic -> semantic gap. There's a green lumber problem with this research. We may be able to predict animal responses in playback tests, but we don't have a way to map that back to semantic meaning. This is probably fine for now, but if we don't have adequate semantic theory or if we have multiple competing semantic theories that all explain the patterns equally well, the we're just manipulating the animals, not communicating with them. (eg, It's not even really clear to me that "whale concepts" and "human concepts" would be commensurable.)
(3) Bad incentives. Between media sensationalism, the normal problems and biases that come with funding science today, and potentially terrible usages of "whale tech" (eg, clearing out shipping lanes, warfare), it seems to me there are some extra ethical considerations with this research such that there may be a point where the outcome space is overwhelmingly negative. It would be nice if mechanisms existed such that research could be stopped if these bad incentives activate.