The two most obvious examples I can think of off the top of my head are features like Enums and constructor param visibility settings. Both must be transformed to retain their runtime properties, and both don't exist in any ratified ES spec. Luckily enough they both also happen to have fairly straightforward mappings to their respective JS implementations, and once you know that they do introduce runtime behavior (and it's fairly easy to notice that they do), you can simply avoid them, so the practical impact of these more obvious cases can be limited.

More troubling cases do exist though. I vaguely remember once coming across some obscure runtime behavior for decorators where they attach runtime metadata that's supposedly used for type reflection, which is a runtime effect that's definitely not immediately obvious or intuitive. This and other potential obscure edge cases like it, some of which may exist in TypeScript today and some of which might be introduced in some future version, are part of what makes Flow's focus on providing trivially removable static typings on top of spec-compliant JavaScript so attractive to me (in addition to opening up the option of minimizing the surface area of your transpilation step or skipping transpilation altogether).