The logo is basically a big pill and the tagline "Powerful keep-awake utility" which is clearly alluding to the drug. https://imgur.com/a/RJXHaBa
This was consistent with the feedback the author received: "[the] app appears to promote inappropriate use of controlled substances. Specifically, your app name and icon include references to controlled substances, pills"
Almost all of the other top apps in the app store in the same category use some reference to caffeine either in the name or tagline or description (e.g. "Jolt of Caffeine" or "Owly" which has a logo of an owl in a cup of coffee) https://imgur.com/a/yySBqEL
There's one other, much less popular app called "Coca" which appears to reference cocaine, but doesn't also have a drug-referencing icon or tagline, and which only has 15 reviews. By comparison, Amphetamine seems to be the most popular result, at least for the search term "awake", with 1.37K reviews
The guideline in question doesn't seem to consider excessive use of caffeine as problematic to encourage. "1.4.3 Apps that encourage consumption of tobacco and vape products, illegal drugs, or excessive amounts of alcohol are not permitted on the App Store. Apps that encourage minors to consume any of these substances will be rejected. Facilitating the sale of marijuana, tobacco, or controlled substances (except for licensed pharmacies) isn’t allowed."
Overall, Amphetamine did seem to be pushing the drug-use angle much harder than other apps in the category based on the logo, tagline and title, especially if you consider caffeine abuse not problematic.
Added: I don't have a strong opinion on this one either way, other than edgy naming has pros and cons. Word of mouth is easier, but sometimes a problem like this happens.