Not exactly a scientific debate, but among the general public there was strong opposition to the idea that rocket engines would work in space, where there’s “nothing to push against.” Famously, the New York Times editorial board mocked Robert Goddard (the rocket scientist that now has a NASA space flight center named after him) in a 1920 article:
“That Professor Goddard, with his ‘chair’ in Clark College and the countenancing of the Smithsonian Institution, does not know the relation of action to reaction, and of the need to have something better than a vacuum against which to react — to say that would be absurd. Of course he only seems to lack the knowledge ladled out daily in high schools.”
The New York Times eventually formally retracted that op ed, on July 17th, 1969 - while the Apollo 11 crew was already en route to the moon. The retraction is pretty funny:
Further investigation and experimentation have confirmed the findings of Isaac Newton in the 17th century and it is now definitely established that a rocket can function in a vacuum as well as in an atmosphere. The Times regrets the error.