Well, Marxist historiography is pretty broad. Since Marxists do not necessarily have a shared theoretical framework (beyond some very vague commitments), nor are they all specialists in the same field, it makes more sense to ask for criticisms of particular authors in a particular field.

Since Robert Brenner's work on early modern European economic history has been particularly influential, probably more so than most Marxist approaches, I think it's fruitful to start there. Brenner's most important essays are "Agrarian Class Structure and Economic Development in Pre-Industrial Europe" (1976), "The Agrarian Roots of European Capitalism" (1982), and "Property and Progress" (2007). Important non-Marxist critiques of Brenner can be found in: Allen, Enclosure and the Yeoman (1992); Epstein, Freedom and Growth (2000); Whittle, Land and Labour in Norfolk 1440-1580 (2000); and of course many of the various responses to Brenner in the 1985 anthology appropriately titled The Brenner Debate.

edit: Forgot to add Hatcher & Bailey's Modelling the Middle Ages (2001), which has a chapter specifically critiquing Marxist models.

It's definitely not modern by any stretch, but probably if you're looking for a work that is a challenge (or a complication?) to a Marxist conception of history, or more specifically Marx's conception of history and historic materialism, then probably start with Max Weber's The Protestant Ethic and the Spirit of Capitalism, since it makes the case that, rather than as Marx would have it, cultural concepts can shape material conditions and economic systems. It's also a very foundational text on its own, and also one that gets massively mis-paraphrased.