Late in the game and perhaps missing the point, but in order to try and understand for myself...
Your objection was that you:
(1) followed the 'method' or 'ideal' as (2) well as possible
(3) ended up with a hypothesis that was factually incorrect
(4) risked of 'wasting' a very long time researching something that ended up being wrong
(5) that the 'method' or 'ideal' does not help one to avoid this properly
(6) all of which combined make the method/ideal problematic as it is likely to statistically to also result in a high number of 'wasted years researching something useless' (or some variation of that)
Now, there are many ways to look at this argument.
In reference to (1) and (2): Ideal can only be approximated, but never achieved. We do as well as we can and improve (hopefully) through every trial and error
ref (3): How did you find out this was 'wrong'? Are you sure? Can you prove it? If so, the question boils down to: how can one lower the likelihood of working on something 'wrong' for too long? A common suggestion is to share ideas even when they are being worked on: open them up for testing and attack by anyone, because a million eye balls will do it better than two (assuming the two are within the million). A second suggestion is to work with multiple simultaneous hypotheses all of which according to the ideal support current data, have predictive power, are falsifiable (via experiments) and are divergent enough as to be considered separate.
(4) How can we know the length of time if we have not 'wasted' it? How can we know the 'waste' if we have not walked that path of knowledge? I would propose that anybody who diligently, openly and humbly follows the ideal to the best of her skills will arrive at lot of 'non-wasted' knowledge, models, thinking, publications, prestige, colleagues, positions, etc - EVEN if the whole hypothesis in the end is falsified. Just look at theoretical physics and the amount of silent evidence in the graveyard of falsified hypotheses, many of which were done by intellectually towering giants and branched off into new research areas in maths, statistics, meta-theory and philosophy. I'd love to attain a wasted failure like that myself :)
(5) This is the biggest argument. In theory I agree, in practice not quite so. Of course, the ideal method does not guarantee lack of such 'failure' (which it is not, imho, as argued above), but skillful implementation of this method can lower such a likelihood, but it requires, imho, humility, openness and and constant fight against bias, something which we can never be free of, but can temporarily be aware of.
(6) Too big to tackle in a post, at least for me :)