When Napoleon was considering building the Suez canal his surveyors repeatedly measured the Red Sea being 9 meters higher than the Mediterranean. Considering this was more than a century after Newton why was it not clear to them that such variations in sea level are not possible?

To put it simply, it is a case of "to see is to believe." Sure, the law of Universal Gravitation was there, but that does not translate to every person being well-educated and of full understanding of its implications. To make a comparison, the theory of Relativity has been around and established for over a century, but the average person would have difficulty wrapping their head around the idea that two people could experience the passage of time at different rates or that the core of the Earth is technically 2.5 years behind the crust on the grand scheme of things.

Measurements were taken (erroneously and in fragments, during wartime) and they stated there was a difference in water levels. It was seen (erroneously), and thus believed, by those at hand. End of the question.

It should also be made clear that the issue wasn't as simple as Napoleon hearing the news and throwing the idea in the trash until Bourdaloue rolled into town around half a century later and reinstated Newtonian physics. For Napoleon, the idea was let go forcibly when the French army evacuated Egypt in 1801. The Institut d'Égypte and the "savants" were evacuated with them, only a couple of years into their appointment to essentially catalog Egypt. He had no control of the region and his savants had only fragmented and unfinished notes to work off of. When the dust settled from the French occupation and Muhammad Ali's rise to power, attention would return to the canal in 1819 as the Mahmoudiyah Canal was dug from the Nile to Alexandria. In 1830 Francis Rawdon Chesney, A British artillery general, would research and submit a report on the feasibility of a canal to connect the seas, in his measurements it was confirmed that the seas were in fact at the same level, but the report was essentially set aside as there was more interest in his idea for an overland route through the Euphrates. The East India Company would support and finance his exploration of such a route, which would turn out to be quite a difficult excursion for a variety of reasons, but would ultimately result in a route successfully established around 1837. This would remain relevant to the discussion as the British vastly preferred the idea of this route that they had full control over to the potential of an open canal to interfere with their Indian trade. Meanwhile, Linant de Bellefonds, who became Egypt's Chief Public Works Engineer, would set about comprehensively surveying the Suez isthmus and would be drafting his own plans for a Suez Canal in the early 1830s. Other interests such as French reformer Barthélemy Prosper Enfantin and Austrian railroader Alois Negrelli would express interest and try to turn Muhammad Ali around to the idea. Enfantin would of course found a society in 1846 to gather a great deal of influential people to turn their attention and studies to the project and there's where we come to Bourdaloue finally publishing his survey of the region that would foster that general acceptance that the bodies of water were in fact at the same elevation and was in fact practical.

So to sum it all back up, one must remember a few key points to understand why people did not immediately question the idea and why it took so long for a credible proof to sway people. First, the measurements appeared to come from a credible source despite the reality. Second, while the science had been established, that is not synonymous with it being commonly held and understood fact. Third, the region was engulfed in a good deal of turmoil and geopolitical conflict, major public works like a ~200km canal were not at the forefront of minds and there was a lack of serious focus on the idea. Finally, There were, in fact, numerous parties who believed the seas were even as well as made preliminary surveys to confirm this and there were plans predating Bourdaloue's by over a decade. The powers that pulled those triggers were just not expressing the interest, or in the case of Chesney, were likely intentionally burying the matter in the interest of preserving their control of trade across the region. The Suez canal was (perceived as) bad for British business, the Egyptians were under leadership that opposed foreign influence, and the French had lost access to the region.