It's worth noting right away that Scientism is self-defeating, for it is not itself an empirically verifiable thesis. Insofar as its proponents have any reasons at all for advancing the view, they are engaging in (bad) philosophical, not scientific, reasoning. This is the familiar point that one cannot assess philosophy (even negatively) without thereby engaging in philosophy oneself. [For a more positive argument in support of the a priori, see my post on conditionalizing out all empirical evidence.]
This bias against philosophy is unfortunate for the obvious reason that there are a lot of interesting and important philosophical truths, which the scientismist would never think to look for. (My original 'scientism' post quoted some ignorant dismissals of Nick Bostrom's very interesting 'Simulation argument'. Not that I think his conclusion is true; but it is eye-opening just to consider.) Moreover, as I once wrote:
All your “common sense” beliefs rest on philosophical assumptions. Most people prefer not to examine them, but that doesn’t mean they aren’t there. It just means that everything you think and do could be completely misguided and you wouldn’t even realize it.
The scientismist will no doubt have many false philosophical beliefs in addition to their scientism. (We all do.) But if they are unaware of the rational tools that allow us to identify and correct such errors, then they will be stuck with them -- not a situation that any dedicated truth-seeker would consider desirable.
I think it's especially unfortunate that most folk seem unaware that reasoned inquiry into normative questions -- e.g. ethics and political philosophy -- is possible. This is at least part of the explanation why public discourse on these matters is so impoverished and sub-rational. So I think it's very important for more people to appreciate that we can go beyond mere instrumental rationality and also assess one's ultimate ends in terms of rational coherence.
Scientism also leads to more mundane mistakes. For example, in a recent 'Overcoming Bias' thread, one commenter defended the common-sense view that different observers experience the same colour qualia (rather than my 'red' being your 'yellow'), on the grounds that the alternative claim is "purely metaphysical with no implications for reality". But that can't be the right reason, because the same could be said of the eminently reasonable -- and presumably true -- view that he was defending. Whether we experience the same qualia or different, either answer is "purely metaphysical" with no scientific implications. So the right justification for the former view must lie elsewhere (e.g. in philosophical principles of parsimony that count against drawing unmotivated ad hoc distinctions).
Fortunately, this bias is easily overcome. Accept no substitutes: Think!
[See also: The Problem with Non-Philosophers.]