To use an example that a regular human would be familiar with: what if the aliens knew math and physics... and were basically ultra-nazis, and very happy to just subjugate you because "our nazi philosophy says that we are superior to everyone else and you are inferior to them" and put you in concentration camps as factory labor for their war machine? You have your own reasons for studying science and math, but what if their entire reason for studying science and math was to build rockets to kill others?

This seems extremely likely, actually! The vast majority of human history has been filled with autocratic governments that centralized power, not free democracies. From the sample size that we have in history, most of the time when the natives meet a stronger scientific power... has not gone well for the natives. What makes you think it will be any different if you meet an alien?

What makes you think just knowing math and physics means that the intelligent alien would be "good" by modern human standards?

And this is just standard boring political talk! We understand that from human politics! What if it's STEM-y and the aliens decide to say "we are killing all of you and slicing all of you into thin slices to scan, in order to scan you into training a LLM"? That sentence would not even be in human thoughtspace 10 years ago! There's almost certainly an even weirder concept that humans today do not have words for, which may be a strong motivation for aliens or even their primary motivation!

I am not an english major, by the way. I am a typical engineer with a strong STEM background, who has happened to have absorbed enough sci-fi concepts through osmosis. I do not consider it likely that we will meet aliens in our lifetime, but I do not expect aliens to follow modern human standards of behavior.