Not using indent settings from .vimrc?

[dnd]

I installed the plugin using pathogen. It didn't seem to use the ftdetect script, so I manually placed the command in my .vimrc, and then syntax highlighting started to work.

The indentation though doesn't work at all in html, js, or css. It seems to be doing some combination of tabs and spaces. In my vue file verbose set shiftwidth? = 8, and verbose set expandtab? = noexpandtab. If I check those values in an html or javascript file, I get verbose set shiftwidth? = 2, and verbose set expandtab? = expandtab and it shows that it was last set in my .vimrc

Any ideas what might be going on, or where I should start looking for the problem?