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The claim that we could see virtually empty oceans by 2048 was sourced from a projection contained in the paper: ‘Impacts of Biodiversity Loss on Ocean Ecosystem Services’ author Boris Worm (a marine conservation biologist) et al (reference below). This projected that all the world’s commercially exploited fish species would have experienced collapse by 2048 (based on the extrapolation of regression in Fig. 3A to 100% in the year 2048), i.e., that to continue to commercially exploit these populations would become impossible by 2048.
https://news.stanford.edu/news/2006/november8/ocean-110806.html

Critics of the film have said that this projection date was corrected in the 2009 paper ‘Rebuilding Global Fisheries’ (reference below), authored by Worm and others, including fisheries scientists (who analyse marine populations from a business perspective using measurements such as maximum yield from fisheries rather than markers of species conservation by marine conservationists). The 2009 paper does not correct, but rather cites the earlier paper, showing that some rates of decline had slowed since 2006 (in ‘5 out of 10 ecosystems‘) but that 63% of assessed fish ‘stocks’ worldwide ‘required rebuilding’. Furthermore, fish populations in places with little management capacity – mainly the developing world and constituting a majority of fish landed – are faring much worse than those with better resources for management.
(https://science.sciencemag.org/content/sci/338/6106/517.full.pdf ). 

In summary, the 2006 study has not been corrected or retracted, and has been cited over 3,000 times. Many of its critics are industry-funded, including the most quoted author Professor Ray Hilborn, who, according to his own website, receives funding from the fishing industry. (according to Greenpeace over $3.5 million: https://www.greenpeace.org/usa/research/overfishing-denier/; his industry funding was largely undeclared until the Greenpeace investigation)
https://t.co/a3gS0hDQQR?amp=1

In 2016 Boris Worm in his paper ‘Averting a Global Fisheries Disaster’ again found the outlook very poor, summarising that population health had in fact declined since his original study, and that 88% of ‘stocks’ would be overfished and well below their target biomass by 2050.
https://www.pnas.org/content/113/18/4895

Further, in 2018, the Secretary-General of UNCTAD (Mukhisa Kituyi) and the UN Secretary General’s Special Envoy for the Ocean and Co-Chair, Peter Thomson reported that nearly 90% of typical fish stocks in the oceans will be gone by 2050 (link below), saying global subsidies for large commercial fishing must stop.
https://unctad.org/news/90-fish-stocks-are-used-fisheries-subsidies-must-stop
https://www.weforum.org/agenda/2018/07/fish-stocks-are-used-up-fisheries-subsidies-must-stop/

Lastly, in 2020, an FAO report used figures up to 2018 which show that 59.6% of fish stocks are "maximally sustainably fished" and 34.2% of stocks are "fished at biologically unsustainable levels". In summary, 93.8% of fish stocks are either biologically unsustainable or at their maximum level of exploitation. 
http://www.fao.org/fisheries/en/

There is a problem of moving goalposts that is unacknowledged in most of the above assessments: the target stock size at which a fishery is considered to be sustainable has been lowered over the last couple of decades by fisheries scientists. This means that without any improvement in management, more fish stocks are considered sustainable today than they were three decades ago
https://academic.oup.com/icesjms/advance-article/doi/10.1093/icesjms/fsaa224/6050569?login=true

The outcome of this altered approach –which lacks a sound basis in ecological science – is that fishing is more risky, with a greater probability of causing population collapse, has more impacts on the environment and ocean health, and reduces resilience of ocean ecosystems to global change.

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