People often say "LISP is so powerful but nobody can understand anyone else's code". That's the dominant explanation for why LISP isn't more popular (along with the "oatmeal with toenail clippings mixed in" syntax, which most people don't find readable, regardless of the fervent beliefs of the LISP community to the contrary). The community stays small because of the unappealing syntax, and even within the community people find it hard to work together, because everyone has their own style, so the kind of coding and collaboration that produces generally useful libraries doesn't tend to happen. I would argue there's no meaningful distinction between "bad habits" and "habits that inhibit the development of generally useful software". In fact, that's the most useful definition of "bad habits" I can imagine.

Flexibility is a root cause of bad habits thus defined, because flexibility is what enables people to make bad choices. Language designers have long recognized this. It's why certain languages impose heavy restrictions on how you can structure your code, from Java's everything-is-a-class to Python's indentation-based scoping. They have a certain vision for what constitutes effective code and they know it won't happen unless they force everyone to follow it. In other words, they choose to reduce flexibility to prevent what they consider to be bad habits.

> R encourages bad habits for the following reasons:

Your reasons are just common complaints about R issues, not actual arguments that these issues encourage bad habits.

> - R is made "for statisticians, by statisticians" so a lot of the example code out there is very poorly written

At best this is an argument that widely publicized badly written R code encourages bad habits, not R itself.

> There's also the 1 indexing

There's a big difference between "language feature I don't like" and "language feature that encourages bad habits". A language that has different conventions than your favorite language is just different.