I don't think there are any works of Marx dealing with Kropotkin, perhaps there exist some small remarks amongst the thousands of pages of his writting but I personally doubt that. Kropotkin and Marx also do not seem to have ever met personally (Kropotkin, for example, does not mention any meeting with him in his memoirs).

Because of this I will focus on how Kropotkin felt about Marx and his work, since he was obviously aware of Marx and his writings and while he never dedicated a full work on him there are still some instances were he mentioned him. Thru those we can see that Kropotkin considered Marx works to be unscientific, starting at the usage of the dialectic method which Kropotkin completely rejected:

We have heard much lately of the dialectical method which the social democrats recommend to us for the development of the socialist ideal. But we completely reject this method which, moreover, is not accepted by anyone in the natural sciences. This “dialectic method” reminds the modern naturalist of something very antiquated—from a past-life and, thankfully, long since forgotten by science. None of the discoveries of the nineteenth century—in mechanics, astronomy, physics, chemistry, biology, psychology or anthropology—was made by the dialectical method. All were made by the inductive method—the only scientific method.

He also talked about "the many economic errors into which socialists have lately fallen, as a consequence of their predilection for the dialectic method and economic metaphysics, which they have resorted to instead of applying themselves to the study of the actual facts of the economic life of nations".

Kropotkin at one point, in a rather damning way, compared his rival on the subject of biology, August Weismann, to Marx calling him "the Karl Marx of biology, just as superficial, making grandiose generalizations on a handful of facts [and] metaphysics on a foundation that does not stand up".

He also remained unimpressed by Marx' Magnum Opus "Das Kapital" writing in a letter that it "is a marvellous revolutionary pamphlet but its scientific significance is nil".

Marx political economy could, for Kropotkin only „take the definitions of metaphysical and bourgeois political economy and say: 'You can see that even accepting your definitions, we can prove that the capitalist exploits the worker!' Which sounds good, perhaps, in a pamphlet but it has nothing to do with science“.

Kropotkin rejected the labor theory of value, rejected likewise the extraction of surplus value as the main evil of the capitalist system and also criticized Marx distinction of qualified and simple work.

To finish this I'd like to quote Caroline Cahm who summed up Kropotkins criticisms of Marx in the following way:

Marx and Engels, in confining themselves to the dialectical method in their study of human society and political economy had failed to provide real scientific proof for any of their affirmations about so called scientific socialism.[...]

The basic tenet of historical materialism that bourgeois society was going to give birth to socialism, apart from being essentially determinist and therefore exercising an inhibiting effect on the action of revolutionaries, was based on a false claim about the inevitable concentration of capital which had been discredited by the observations of Cherkesov and others. Marx's theory of value was a naive formulation based on Ricardo's assertion of a direct relationship between labour and value, which, in the elaboration of the idea of surplus value, failed to recognise the real cost of labour measured in terms of poverty and deprivation; and the evil of the present system was not that there was a surplus value of production which went to the capitalist but that there should be any surplus value at all. As regards his socialist ideas Marx had simply used hegelian dialectics to repeat what the utopian socialists had said so well before him. He had failed to break free from the old metaphysics and his followers, the social democrats, bogged down in abstractions which hid careless analysis, had gone on repeating the formulas of progress their master had believed to be vaguely true fifty years before, without verifying or exploring them

Sources:

Most of the quotes by Kropotkin come from his work „Modern Science and Anarchy“ a new version of which, edited by Iain McKay, has recently been published and it's the one I'm using here. I found the quote on Weisman in Eric M. Johnsons Dissertation "The Struggle for Coexistence: Peter Kropotkin and the social ecology of science" which is also worth a read if one is specifically interested in Kropotkins biological ideas. The book by Caroline Cahm is called "Kropotkin and the Rise of Revolutionary Anarchism" it's also were I got the quote on "Das Kapital" from. Kropotkins criticism of the labor theory of value can most notably be found in "Modern Science and Anarchy“ Chapter „XIV. Some Conclusions of Anarchy", criticism of Marx theory of exploitation and his distinction of qualified and simple work also appears in "The Conquest of Bread".