Where to put routines in Django project?
Placing additional python files alongside your settings.py should not create migration errors in the normal case. Are you sure these files are causing the errors?
To you question:

If you will use those functions inside a single app, you could create a subdirectory inside that app, for example utils; it should be on the same level as the migrations and templates directories of the app.
However, if you will be using those functions inside many apps you could create a new app without models and migrations, lets call it custom_utils, in which you can place all your functions.
I have rather vast implementation of functionality needed for processing specific type of data stored in my Django DB (7 interconnected files containing ~100 lines of code each). There's a facade method in one of those files that I call from related method in views.py so that there is no mess inside of views file.  
For now I put everything inside a new folder in the same directory where settings.py urls.py and wsgi.py are, but now every time I'm calling makemigrations I receive a handful of unrelated information that has nothing to do with changes in data model.
What is the best place to store those routines?