There have been a few catastrophically bad calls by govt science advisers (and some very good ones, but that's not what you asked).
The first science mistake was that all the underlying technical planning for a respiratory infectious disease epidemic was just wrong. It was based on the idea that you could mitigate and manage the spread of an epidemic virus through the population without lockdowns (what later became known as a 'herd immunity' strategy - which I think is a slightly misleading name, but it is clear that the original strategy was a mitigation strategy, not the suppression strategy we ended up with). However nobody had worked through the implications of this for the NHS until we saw the healthcare system breakdown in Italy. There was no possibility this kind of strategy could ever have worked, even for 'flu, without a total NHS collapse because the numbers of people needing hospital care would always have been too high. This could and should have been recognised in all the years we had to plan for this. My guess is that public health planners also assumed that suppression would be politically unpalatable - but crucially this was not their call to make and they should always have had a suppression option on hand for ministers instead of ruling it out at the planning stage. This is a very tragic example of why officials shouldn't build political judgements into their technical advice.
The costs of this underlying mistake were very high, because it meant that we moved straight into implementing a suppression strategy without having time to plan it properly. All social distancing/lockdown rules had to be thought up and implemented at lightning speed, and that inevitably meant that all the moral and practical implications of lockdowns were not thought through properly.
The secondmistake was the scientific assumption that there would be no asymptomatic transmission. This was what the decision to discharge people from hospital into care homes was based on, and this had all-too-well-known tragic results for some of the most vulnerable people in the country. This was again a totally avoidable mistake (there are plenty of viruses that transmit asymptomatically) where scientists should have been more conservative.
Thirdly, the risk of new variants and the risk they posed to vaccines - the speed of the emergence of Alpha in late 2020 caught scientists totally by surprise and we are simply lucky that vaccines have worked against every variant so far.
Finally, the modelling. I think the modelling was correct at the start, but then it is always easiest to model an epidemic at the start. As time has gone on, I think it is clear that there is some fundamental transmission dynamic of the virus that we don't understand. This is why still none of the modelling explains the sudden drop in cases from the summer peak last year.
Some of the messaging, particularly on Covid being airborne, has been pretty bad, but that is more of a science communication problem rather than a problem with the scientific consensus itself.