I had setup a custom block type with a link field. I created a block instance with it.
It looks like even without assigning that block to a region it produces errors and makes the front-end of the site render without its theme. The messages:
Notice: Undefined index: path in link_field_formatter_view() (line 376 of core/modules/link/link.module).
Notice: Undefined index: options in link_field_formatter_view() (line 377 of core/modules/link/link.module).
I'm not absolutely sure these notices are the cause for the theme not being rendered. I can't delete the block using the link field so bit hard to reproduce.