Some templates are only used to include metadata, e.g. categories. In this example http://en.wikipedia.org/w/index.php?title=Ashton_Agar&oldid=564224425&veaction=edit the document starts with two such categories, producing linebreak characters, with templates spanning 0 characters in between (accessible still be cursoring). An uninitiated user may just decide to delete this whole line at the the top, thus removing the hidden templates.
Perhaps we need to detect if a template contains no meaningful content and then move it into the metadata so it can't be accidentally deleted. We'd also need a UI for editing them though.