It's obviously not the case that we can hold Marx responsible for what was carried out in his name (I'd be happy to point you to Marxist analyses of how the USSR differed from Marx's limited notes on praxis) and it is the case (if one is familiar with the literature) that Marx is treated with skepticism, and Freud probably doubly so.

PhDs and research in political economy, critical theory and sociology - the three most "Marxist" disciplines one can name at universities - are awash with criticisms of Marx, either major or minor. In fact, there seems to be more people criticising (or at least amending) his work than there are still people defending it. This is especially true in the analytic side of political economy, in which many researchers believe (rightly or wrongly) that the last vestiges of Marx have been finally cut off by Sraffa, and the most we can hope for is Ricardian socialism or social-democratic reform. The very author of the piece we are commenting on has published amendments to Marx's consideration of the theory of value in an attempt to dissolve the transformation problem. Even Marxists (considered as those with an affinity to Marx who reject a few or some of his theses) themselves disavow Marx to various degrees - either in his theory of value (Sraffa, Yoshihara, Roemer, perhaps Okishio) or his construction of historical materialism (Elster), the transformation problem (Laibman, Mohun, Veneziani). In fact, the number of people who hold that Marx was absolutely correct and that interpretation can save him from criticisms since the 60s is vanishingly small, though it does wield some influence - Kliman, McGlone, Carchedi, Freeman, Moseley, Patrick Murray. But all of the figures I have mentioned engage in critique and counter-critique of each other, sometimes even stretching to the mean-spirited. They are not isolated or refusing to engage on dogmatic principles. Even the most ardent defenders of Marx to the letter are accomplished academics, often professors of philosophy or economics, with PhDs and tenure.

On the matter of Freud I'm not so familiar other than to point out that psychoanalysis is not psychology and it is not taken as part of psychology. The question of whether it qualifies as science or not, or whether it can become scientific (in its post-Freud incarnations) is still debated. But criticisms of Freud are everywhere, not least from actual philosophers in psychoanalysis - Feminist philosophy has been very critical of Freud, for example. Extremely influential philosophers in the continental tradition have been critical of Freud - Deleuze and Guattari, for example.

It's not at all fair to say that Freud and Marx, at the least, are not treated with skepticism, even in the disciplines they are most popular in. Outside of those disciplines they are dismissed, and in my opinion, dismissed out of hand. They do not hold some great sway that makes them unquestionable today. There may have been a time at which that was true (perhaps when Das Kapital was being used as a textbook at some Japanese universities in the 20s and 30s) but it is certainly not true today, at lesat if we consider published research rather than the (sometimes misguided) opinions of students who may cling dogmatically to Marx and Freud or to anti-Marxists Karl Popper.