... saving my template as a indt, and after some changes and saves its suddenly a document called indt.
How did you determine it's a 'document called indt'? Do you mean your document's file name is "indt", no more? (That'd point to a buggy script.)
Docs and templates are the same, the difference is just the file extension.
Experiment: take one of your InDesign documents, change the file extension to .indt. ID will by default open it as an unnamed copy (and so will scripts, unless told otherwise). Rename any of your templates to .indd and ID will treat it again as a document.