If we look back to when the term "transpiler" was made popular (not necessarily coined), it is fairly widely acknowledged that it was through CoffeeScript, which defined itself as such. In a sense, I think CoffeeScript was right (or at least not wrong) to define itself as "transpiler" rather than "compiler". After all, it was a syntax tree to syntax tree transformation, technically involving no more than a parser and a pretty-printer (not saying there's anything wrong with that).
However, because CoffeeScript was the first language to compile to JavaScript, swaths of developers have associated the term "transpiler" to "compiles to JS" or "compiles to another language that also happens to be used as source language". Now, all these developers will systematically refuse to call TypeScript, ClojureScript, Scala.js, etc. as "true compilers" (let me list a few more in alphabetical orther so I'm not perceived as totally biased: BuckleScript, Elm, Flow, Kotlin, PureScript). Instead they insist on calling them "transpilers" and associating their characteristics to that of CoffeeScript.
Now that CoffeeScript is falling out of favor (in part because most of what it brought to the table has been picked up by ES2015), this category of developers associates any kind of language that compiles to JS as a thing that no one would ever want to use. Worse, they will often consider such languages as insults to their craft. "Why don't you just learn JavaScript and code in it?", they ask. This is a cultural problem, because this mindset prevents from even considering what other languages can bring to them.
Technologically speaking, there is absolutely nothing separating ClojureScript/Scala.js from Clojure/Scala. The former compile to JavaScript; the latter to JVM bytecode; but the amount of compiler engineering that go into all these compilers is basically the same. However, somehow, culturally, they are fundamentally different: ClojureScript/Scala.js devs should just learn JavaScript, while it's OK for Clojure/Scala devs not to "learn Java".
In the end, the existence of the term "transpiler" has a negative effect on the perception that many developers have on the quality of languages that compile to JS. You will often read things like "such transpilers always leak JavaScript in the end", which is simply not true for ClojureScript and Scala.js. Or "interop with JS libraries is always an issue with transpilers"; again, not true. And those misconceptions make them reject and bash on similar technologies, for no good reason.
And that is why I loathe the term "transpiler".