The main difference was that the Warsaw Pact had a single mandated epistemology: the dialectical materialism of marxist and leninist philosophy. I'm told this is fairly workable as a framework for science, but it also represents a fundamental restriction.
Still, I can't think of any substantial disagreements in physical science except for the ones you mentioned. There were many in softer fields, such as economics, prehistory and anthropology.
I know a few people who did medicine, IT, philosophy and history of religions in the Warsaw Pact. (No biology or geology, sorry.) All describe there was infrequent but regular communication going on with the scientists in Imperialist countries. It was tightly controlled, i.e. only a few selected and carefully briefed scientists would be allowed to visit conferences abroad. But that doesn't seem to have been about heretical knowledge, but about the loyalties of the scientists. Many would defect given the chance, and the Warsaw Pact countries tried hard to prevent that. (For example, your chance of attending a conference outside the Iron Curtain would much depend on whether you had close family staying at home that you wouldn't want to abandon.) A few more would have access to the locked bookshelf with the foreign journals and books by persona non grata authors like Nietzsche, but those journals and books did get read.
This was important in cases such as the rise of the HIV threat. The Warsaw Pact heard about it long before it had any cases of its own, because there was little tourism, even less organized crime (due to the worthlessness of their currencies) and a tradition of central registration of STDs that would have been called draconian in the West at that time. When HIV did trickle into the Warsaw Pact, its health system was prepared.
I can think of one case where the relative isolation was an advantage. In the fifities, West German pharmacologists offered East German ones to try Thalidomide, a sedative used, among other things, for morning sickness in pregnant women. The East Germans looked at it and refused, saying they thought it dangerous for foetal development. So the thousands of cases of phocomelia that followed were all in Western Germany.
Do you have a detailed source for the story about Thalidomide? (in German is OK) America rejected it, too, but as far as I can tell, for no reason that actually would have detected the problem. So the detail I'm wondering about is whether the East German rejection actually singled out pregnancy.
What can we learn about science from the divide during the Cold War?
I have one example in mind: America held that coal and oil were fossil fuels, the stored energy of the sun, while the Soviets held that they were the result of geologic forces applied to primordial methane.
At least one side is thoroughly wrong. This isn't a politically charged topic like sociology, or even biology, but a physical science where people are supposed to agree on the answers. This isn't a matter of research priorities, where one side doesn't care enough to figure things out, but a topic that both sides saw to be of great importance, and where they both claimed to apply their theories. On the other hand, Lysenkoism seems to have resulted from the practical importance of crop breeding.
First of all, this example supports the claim that there really was a divide, that science was disconnected into two poorly communicating camps. It suggests that when the two sides reached the same results on other topics, they did so independently. Even if we cannot learn from this example, it suggests that we may be able to learn from other consequences of dividing the scientific community.
My understanding is that although some Russian language research papers were available in America, they were completely ignored and the scientists failed to even acknowledge that there was a community with divergent opinions. I don't know about the other direction.
Some questions: